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Software RP Name ✨Software Type ✨Software Class ✨Research Field ✨Research Area ✨Research Discipline Software Description ✨Core Features ✨General Tags Software's Web Page Software Documentation Example Software Use RP Software Documentation Version Info ✨AI Description ✨Example Use
7z Ookami Archiver Utility General General 7-Zip is a file archiver with a high compression ratio.
Description Source: https://www.7-zip.org/
7-Zip provides a high compression ratio, supports various archive formats including 7z, XZ, BZIP2, GZIP, TAR, ZIP, and WIM, has a powerful file manager and command-line version, offers AES-256 encryption, and is open-source software. File Archiver, Compression, Encryption https://www.7-zip.org/ https://www.7-zip.org/ https://www.youtube.com/watch?v=N48Z0nG0bcQ Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 22.01 7-Zip is a file archiver with a high compression ratio. It supports several archive formats and can be used to compress and decompress files efficiently.
abacas Anvil Genome Assembly Bioinformatics Biological Sciences Genetics Biological Sciences Abacas is a tool for algorithm based automatic contiguation of assembled sequences. Contig assembly, scaffolding, reference genome utilization Bacterial Genome, Genome Assembly https://abacas.sourceforge.net/ https://abacas.sourceforge.net/documentation.html https://abacas.sourceforge.net/Manual.html Anvil: https://www.rcac.purdue.edu/software/abacas Anvil: 1.3.1 ABACAS is a tool for rapid bacterial genome contig assembly. It takes contigs produced by an assemblrer and scaffolds them to generate a pseudo-chromosome. It can handle multiple contigs and uses reference genomes for scaffolding.
abaqus Expanse Simulation Software Other Engineering & Technology Engineering Engineering & Technology Abaqus is a software suite for finite element analysis and computer-aided engineering, primarily used in engineering and design fields for simulating the behavior of structures and materials under various conditions. It offers advanced capabilities for modeling, analysis, and visualization, making it a powerful tool for solving complex engineering challenges. Finite Element Analysis (Fea), Structural Analysis, Thermal Analysis, Fluid Analysis, Multiphysics Simulation, Explicit & Implicit Solvers, Material Modeling, Contact Analysis, Fatigue Analysis, Nonlinear Analysis Simulation, Finite Element Analysis, Computer-Aided Engineering, Materials Analysis https://www.3ds.com/products/simulia/abaqus https://www.3ds.com/support/documentation/user-guides https://www.3ds.com/products/simulia/training
https://www.youtube.com/watch?v=3-NIKzmhxOU&list=PLz_XdUL-6Y_k-LgmCKo5ejqRAGpfXPk23
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 2018.Bk, 2018, 2021Hf7 Abaqus is a software suite used for finite element analysis and computer-aided engineering simulations for a wide range of industrial applications. It provides powerful simulation capabilities to analyze the behavior of materials and structures under various conditions.
abinit Bridges-2, Expanse, Faster Electronic Structure Calculation Simulation Software Physical Sciences Materials Science Condensed Matter Physics ABINIT is a software suite to calculate the optical, mechanical, vibrational, and other observable properties of materials. Starting from the quantum equations of density functional theory, you can build up to advanced applications with perturbation theories based on DFT, and many-body Green's functions (GW and DMFT).
Description Source: https://www.abinit.org/
Abinit offers a wide range of functionalities for modeling materials properties, such as electronic band structures, total energies, forces, dielectric properties, and more. It supports parallel computing for scalability and efficiency. Materials Science, Condensed Matter Physics, Electronic Structure Calculations https://www.abinit.org/ https://docs.abinit.org/tutorial/ https://docs.abinit.org/tutorial/ Bridges-2: https://www.psc.edu/resources/software/abinit
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Bridges-2: 9.4.2-Intel
Expanse: Q47Zuuw
Faster: 9.4.2, 9.6.2
Abinit is a first-principles simulation software for materials science, condensed matter physics, and related fields. It performs electronic structure calculations based on density functional theory (DFT) and many-body perturbation theory.
abismal Anvil Computational Chemistry Software Scientific Computing Software Other Natural Sciences Sciences Biology Another Bisulfite Mapping Algorithm (abismal) is a read mapping program for bisulfite sequencing in DNA methylation studies. Abismal provides ab-initio solvers for studying intersolute-interaction and surfaces and materials. It includes a library for ab-initio calculations and supports various methods for electronic structure calculations. Ab-Initio, Electronic Structure Calculations, Materials Science https://github.com/smithlabcode/abismal https://github.com/smithlabcode/abismal/blob/master/docs/MANUAL.md Anvil: https://www.rcac.purdue.edu/software/abismal Anvil: 3.0.0 AbInitio Solvers for Intersolute-interaction and Surfaces and Materials with Ab-initio Library
abpoa Anvil Alignment Tool Bioinformatics Biological Sciences Comparative Genomics Genetics abPOA is an extended version of Partial Order Alignment (POA) that performs adaptive banded dynamic programming (DP) with an SIMD implementation. abPOA can perform multiple sequence alignment (MSA) on a set of input sequences and generate a consensus sequence by applying the heaviest bundling algorithm to the final alignment graph.
Description Source: https://github.com/yangao07/abPOA
1. Utilizes a bi-path structure for pairwise sequence alignment
2. Designed for aligning long noisy read sequences
3. Adapts to local alignment conditions to improve accuracy
4. Efficient and scalable for handling large datasets
Multiple Sequence Alignment, Sequence Alignment, Long Read Sequences https://github.com/yangao07/abPOA https://github.com/yangao07/abPOA#general-usage https://github.com/yangao07/abPOA/blob/main/example.c
https://github.com/yangao07/abPOA/blob/main/sub_example.c
Anvil: https://www.rcac.purdue.edu/software/abpoa Anvil: 1.4.1 ABPOA (adaptive bi-path overlap aligner) is a multiple sequence alignment tool that employs a novel bi-path structure to generate pairwise alignments between sequences for constructing a multiple sequence alignment. It is designed to align long noisy read sequences efficiently and accurately by adapting to local alignment conditions.
abricate Anvil Tool Bioinformatics Biological Sciences Sciences Biology Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB. Identify Antimicrobial Resistance Genes, Detect Virulence Genes, Analyze Bacterial Genomes Antimicrobial Resistance, Genomic Analysis, Bacterial Genomics https://github.com/tseemann/abricate https://github.com/tseemann/abricate Anvil: https://www.rcac.purdue.edu/software/abricate Anvil: 1.0.1 abricate is a tool for finding antimicrobial resistance and virulence genes in bacterial genomes.
abseil Aces, Faster Code Library Library Computer & Information Sciences General General Abseil is an open source collection of C++ libraries drawn from the most fundamental pieces of Google’s internal codebase. These libraries are the nuts-and-bolts that underpin almost everything Google runs.
Description Source: https://abseil.io/about/
1. Cross-platform support
2. Robust and well-tested library code
3. Portable and efficient implementations
4. Compliant with C++11 standards
5. Designed to complement the C++ standard library
C++ Library, Open Source, Cross-Platform https://abseil.io/ https://abseil.io/docs/ https://abseil.io/docs/cpp/quickstart
https://abseil.io/tips/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 20230125.2, 20230125.3, 20230802.1
Faster: 20210324.2, 20230125.2, 20230125.3, 20230802.1
Abseil is an open-source collection of C++ code (compliant to C++11) designed to augment the C++ standard library. It provides a set of high-quality library code that is well tested, portable, and efficient for a wide range of purposes.
abyss Anvil, Bridges-2, Faster Hpc Tool Bioinformatics Biological Sciences Genetics Biological Sciences ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
Description Source: https://www.bcgsc.ca/resources/software/abyss
ABySS can assemble very large genomes using paired-end sequencing data. It supports a wide range of input read lengths and allows users to specify the insert size of the library. ABySS is parallelized to run efficiently on High-Performance Computing (HPC) clusters. Assembly, De Novo Assembly, Sequence Assembler, Large Genomes https://www.bcgsc.ca/resources/software/abyss https://github.com/bcgsc/abyss https://github.com/bcgsc/abyss?tab=readme-ov-file#assemble-a-small-synthetic-data-set Anvil: https://www.rcac.purdue.edu/software/abyss
Bridges-2: https://www.psc.edu/resources/software/abyss
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.3.2, 2.3.4
Bridges-2: 2.1.5
Faster: 2.1.5
ABySS (Assembly By Short Sequences) is a de novo, parallel, paired-end sequence assembler that is designed for large genomes and also works well on smaller genomes.
accessusage Expanse Service Developer Support General General Adds ACCESS accessusage tool to paths in the login shell environment. https://software.xsede.org/packaged-software/access-usage-accessusage https://software.xsede.org/production/accessusage/latest/INSTALL https://software.xsede.org/production/accessusage/latest/INSTALL_Testing Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 0.5-1
actc Aces, Anvil, Faster Tool Graph Analytics Computer & Information Sciences General Biology, Mathematics ACTC is a graphics optimization tool that enhances the rendering efficiency of 3D models by restructuring their geometric data. It's particularly useful in applications using OpenGL and Direct3D, where it can significantly improve rendering speed and reduce computational load.
Description Source: https://plunk.org/~grantham/public/actc/README
Identifying Connected Components In Large, Distributed Graphs, Efficient Handling Of Massive Graphs, Scalability Graph Analytics, Connected Components, Distributed Computing https://plunk.org/~grantham/public/actc/ https://plunk.org/~grantham/public/actc/manual.html https://plunk.org/~grantham/public/actc/tcsample.c Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/actc
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.1
Anvil: 0.2.0
Faster: 1.1
ACTC (Assembly, Clustering, and Transformation for Connected Components) is a software tool for finding connected components in large, distributed graphs. It is specifically designed to handle massive graphs efficiently.
adapterremoval Anvil, Faster Bioinformatics Tool Sequence Analysis Tool Biological Sciences Sciences Biology AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. Adapter Trimming & Removal, Identification Of Overlapping Paired-End Reads, Statistics Generation Bioinformatics, Hts Data Processing, Sequence Analysis https://github.com/MikkelSchubert/adapterremoval https://adapterremoval.readthedocs.io/en/stable/ https://adapterremoval.readthedocs.io/en/stable/examples.html Anvil: https://www.rcac.purdue.edu/software/adapterremoval
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.3.3
Faster: 2.3.3
AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data. AdapterRemoval can also identify paired sequences in which both reads overlap after adapter removal and generate a statistics file detailing the results.
adios2 Expanse Library Middleware Computer & Information Sciences Sciences Computer Science ADIOS2 is developed as part of the United States Department of Energy's Exascale Computing Project. It is a framework for scientific data I/O to publish and subscribe to data when and where required. ADIOS2 transports data as groups of self-describing variables and attributes across different media types (such as files, wide-area-networks, and remote direct memory access) using a common application programming interface for all transport modes. ADIOS2 can be used on supercomputers, cloud systems, and personal computers. High-Performance I/O Middleware Library, Simple & High-Level Interface, Efficient Data Management On Parallel Storage Systems, Support For Various Data Formats & Storage Systems, Parallel I/O Operations For Large-Scale Simulations, Scalability & Performance Optimizations I/O Middleware, High-Performance Computing, Data Management, Parallel Computing https://github.com/ornladios/ADIOS2 https://adios2.readthedocs.io/en/v2.10.0/ https://adios2.readthedocs.io/en/v2.10.0/tutorials/basicTutorials.html Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: F2Ejleg, M6X3V7O, ... ADIOS 2 (Adaptable Input/Output System) is a next-generation high-performance I/O middleware library that provides a simple, high-level interface for efficiently managing data on parallel storage systems. It is designed to address the increasing challenges of achieving high performance and scalability when dealing with I/O operations in large-scale scientific simulations and data processing applications.
adol-c Expanse Computational Software Library Mathematics Engineering Mathematics ADOL-C is an operator overloading based AD-tool that allows to compute derivatives for functions given as C or C++ source code. ADOL-C can handle codes based on classes, templates and other advanced C++-features. The resulting derivative evaluation routines may be called from C, C++, Fortran, or any other language that can be linked with C. Automatic Differentiation For C/C++ Code, Efficient Calculation Of Derivatives, Support For First & Higher Order Derivative Information, Useful For Optimization, Sensitivity Analysis, & Uncertainty Quantification Automatic Differentiation, Computational Mathematics, Optimization, Sensitivity Analysis, Uncertainty Quantification https://github.com/coin-or/ADOL-C https://github.com/coin-or/ADOL-C/tree/master/ADOL-C/doc https://github.com/coin-or/ADOL-C/tree/master/ADOL-C/examples Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Hjqerr7, Qygdtvg, ... ADOL-C (Automatic Differentiation by Overloading in C++) is a software package for the calculation of derivatives of given C or C++ code. It allows for the efficient calculation of first and higher derivative information, which is useful in optimization, sensitivity analysis, and uncertainty quantification.
advisor Kyric, Stampede3 Performance Optimization Tool Engineering & Technology Intel Advisor is a performance analysis tool designed to help developers optimize and parallelize their software on Intel architectures. It provides insights for efficient vectorization, threading, and offloading to accelerators, aiding in achieving maximum performance from applications. Performance Optimization For Hpc Applications, Identifying Performance Bottlenecks, Analyzing Parallel Patterns, Recommendations For Performance Improvements Hpc, Performance Optimization, Parallel Computing https://www.intel.com/content/www/us/en/developer/tools/oneapi/advisor.html https://www.intel.com/content/www/us/en/docs/advisor/get-started-guide/2023-1/overview.html Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Kyric: Latest, 2021.1.1
Stampede-3: 23.1, 24.0
Advisor is a comprehensive software tool designed for optimizing HPC applications and maximizing performance on current and future HPC systems. It offers insights into performance bottlenecks, parallel patterns, and potential improvements.
advntr Anvil Bioinformatics Genetic Variant Analysis Biological Sciences Genomics Genetics adVNTR is a tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data. It works with both NGS short reads (Illumina HiSeq) and SMRT reads (PacBio) and finds diploid repeating counts for VNTRs and identifies possible mutations in the VNTR sequences. Utilizes Deep Learning Methods For Variant Detection, Trained Recurrent Neural Networks For Improved Accuracy, Works With Next-Generation Sequencing (Ngs) Data, Efficient & Fast Variant Detection Process Ngs, Variant Detection, Deep Learning, DNA Sequencing https://github.com/mehrdadbakhtiari/adVNTR https://advntr.readthedocs.io/en/latest/index.html https://advntr.readthedocs.io/en/latest/tutorial.html Anvil: https://www.rcac.purdue.edu/software/advntr Anvil: 1.4.0, 1.5.0 Advntr (Adaptive Variant Detection in NGS data with trained Recurrent Neural Networks) is a software tool that utilizes deep learning techniques to identify genetic variants in next-generation sequencing (NGS) data. It employs trained recurrent neural networks to accurately and efficiently detect variants in DNA sequences.
aesara Faster Library Scientific Computing Computer & Information Sciences Engineering Mathematics Aesara is a Python library that allows one to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays. Symbolic mathematical operations, automatic differentiation, optimization, deep learning support Python Library, Symbolic Computation, Deep Learning, Optimization https://github.com/aesara-devs/aesara https://aesara.readthedocs.io/en/latest/ https://aesara.readthedocs.io/en/latest/reference/index.html Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.8.9 Aesara is a Python library for symbolic mathematical operations, particularly focusing on deep learning and optimization. It allows for the creation of complex mathematical expressions and their manipulation symbolically, enabling automatic differentiation and optimization of functions.
aflow Faster Materials Modeling & Simulation Scientific Software Physical Sciences Condensed Matter Physics Physics & Physical Sciences AFLOW is a comprehensive software framework for autonomous density functional theory calculations and materials properties analysis. It offers diverse tools and modules for structure analysis, property prediction, and error correction, including thermodynamic stability analysis and modeling of chemically disordered materials, with public access through the AFLOW website and search API. Some core features of aflow include: 1. High-throughput screening of materials properties, 2. Prediction of phase stability and electronic structure, 3. Automated workflows for DFT calculations, 4. Database integration for materials discovery and design. Computational Software, Materials Science, Density Functional Theory https://aflowlib.org/ https://aflow.org/aflow-school/ https://aflow.org/aflow-school/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.2.11 aflow is a computational software package for first-principles calculations and high-throughput materials science. It enables researchers to study materials properties, electronic structure, and phase stability using density functional theory (DFT) calculations.
afplot Anvil Tool Data Visualization Biological Sciences Genetics Biological Sciences Afplot is a tool to plot allele frequencies in VCF files. 1. Plotting allele frequency distributions
2. Customizable visualization options
3. Supports data from population genetic studies
4. Easy-to-use interface for generating plots
5. Helpful for analyzing genetic diversity and population structure
Allele Frequency, Population Genetics, Genetic Diversity, Data Visualization, Population Structure https://github.com/sndrtj/afplot https://github.com/sndrtj/afplot#Examples Anvil: https://www.rcac.purdue.edu/software/afplot Anvil: 0.2.1 The afplot software is a tool designed for plotting allele frequency distributions, which are commonly used in population genetic analyses and genetic diversity studies. It allows users to visualize the distribution of allele frequencies across a population or a set of individuals.
afterqc Anvil Application Bioinformatics Biological Sciences Sciences Biology Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair. Some core features of afterQC include adapter trimming, read filtering, read trimming, quality control metrics generation, and visualization of QC reports. Quality Control, High-Throughput Sequencing Data, Next-Generation Sequencing https://github.com/OpenGene/AfterQC https://github.com/OpenGene/AfterQC https://github.com/OpenGene/AfterQC#Simple-usage Anvil: https://www.rcac.purdue.edu/software/afterqc Anvil: 0.9.7 afterQC is a quality control tool for high-throughput sequencing data. It performs post-alignment quality control on next-generation sequencing data to provide comprehensive QC metrics and visualizations.
agat Anvil Pipeline Bioinformatics Biological Sciences Genome Annotation Genomics Agat is a suite of tools to handle gene annotations in any GTF/GFF format Genome Assembly Annotation, Evaluation Of Genome Assemblies, Identification Of Genes & Regulatory Elements, Functional Annotation Of Genomic Features Genome Assembly, Annotation, Evaluation, Genomic Analysis https://github.com/NBISweden/AGAT?tab=readme-ov-file https://agat.readthedocs.io/en/latest/index.html https://agat.readthedocs.io/en/latest/agat_how_does_it_work.html Anvil: https://www.rcac.purdue.edu/software/agat Anvil: 0.8.1 AGAT (Annotation-based Genome Assembly Toolkit) is a pipeline designed for comprehensive annotation and evaluation of genome assemblies.
agfusion Anvil Computational Research Tool Biological Sciences Cancer Genomics Bioinformatics AGFusion (pronounced 'A G Fusion') is a python package for annotating gene fusions from the human or mouse genomes. 1. Detection of gene fusions in cancer genomes
2. Annotation and classification of gene fusions
3. Prediction of functional consequences of gene fusions
4. Integration of multiple algorithms for accurate fusion detection
5. Analysis of fusion breakpoints and potential fusion partners
Computational Tool, Gene Fusions, Cancer https://github.com/murphycj/AGFusion https://github.com/murphycj/AGFusion https://github.com/murphycj/AGFusion?tab=readme-ov-file#examples
https://www.agfusion.app/
Anvil: https://www.rcac.purdue.edu/software/agfusion Anvil: 1.3.11 agfusion is a computational tool for annotating and predicting the effects of gene fusions in cancer. It integrates multiple algorithms to identify and characterize gene fusions using RNA sequencing data.
ai Bridges-2 Software Artificial Intelligence & Intelligent Systems Computer & Information Sciences PyTorch AI development environment Core features of AI include machine learning, neural networks, natural language processing, computer vision, and robotics. AI systems can be designed to perform tasks such as speech recognition, decision-making, visual perception, and language translation. Artificial Intelligence, Machine Learning, Neural Networks, Natural Language Processing, Computer Vision, Robotics https://www.psc.edu/resources/software/ai/ Bridges-2: https://www.psc.edu/resources/software/ai Bridges-2: Pytorch_23.02-1.13.1-Py3, Tensorflow_23.02-2.10.0-Py3 AI, or artificial intelligence, refers to the simulation of human intelligence processes by machines, particularly computer systems. These processes include learning, reasoning, problem-solving, perception, and language understanding.
aiohttp Aces, Faster Http Client/Server Framework Web Framework Computer & Information Sciences aiohttp is an asynchronous HTTP Client/Server for asyncio and Python.
Description Source: https://docs.aiohttp.org/en/stable/
Asynchronous Client & Server Components For Http, Websockets Support, Middleware Support For Extending Functionality, Ssl/Tls Support For Secure Communication Python Library, Web Development, Asynchronous Programming https://github.com/aio-libs/aiohttp https://docs.aiohttp.org/en/stable/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.8.3, 3.8.5
Faster: 3.8.1
aiohttp is an asynchronous HTTP client/server framework for Python. It allows for handling HTTP requests and responses in an asynchronous manner, making it ideal for building high-performance web applications.
alfred Anvil Application Productivity Tool Other Computer & Information Sciences Sciences Biology Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner. Customizable Hotkeys For Various Actions, Keyword-Based Search For Files, Contacts, & Web Searches, Text Expansion For Frequently Used Phrases, Clipboard History & Management, Integration With Various Apps & Workflows Productivity, Macos, Keyboard Shortcuts, Automation https://github.com/tobiasrausch/alfred https://www.gear-genomics.com/docs/alfred/ https://www.gear-genomics.com/docs/alfred/cli/ Anvil: https://www.rcac.purdue.edu/software/alfred Anvil: 0.2.5, 0.2.6 Alfred is a productivity application for macOS that boosts your efficiency with hotkeys, keywords, text expansion, and more. It allows users to perform various tasks quickly using customizable keyboard shortcuts.
alien-hunter Anvil Application Bioinformatics Sciences Biology Alien-hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). https://www.sanger.ac.uk/tool/alien_hunter/ Anvil: https://www.rcac.purdue.edu/software/alien-hunter Anvil: 1.7.7
alignstats Anvil Statistical Analysis Tool Bioinformatics Tool Biological Sciences Genetics Biological Sciences AlignStats produces various alignment, whole genome coverage, and capture coverage metrics for sequence alignment files in SAM, BAM, and CRAM format. Statistical Analysis Of Biological Sequence Alignments, Calculation Of Sequence Conservation Scores, Identification Of Conserved Regions, Generation Of Graphical Visualizations Of Alignment Statistics Bioinformatics, Sequence Analysis, Alignment, Statistics https://github.com/jfarek/alignstats https://github.com/jfarek/alignstats https://github.com/jfarek/alignstats?tab=readme-ov-file#usage-examples Anvil: https://www.rcac.purdue.edu/software/alignstats Anvil: 0.9.1 AlignStats is a software tool for the statistical analysis of biological sequence alignments. It provides various statistical metrics and analyses to investigate the patterns and properties of sequence alignments.
all-architectures Ookami Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: All-Architectures
allocations Bridges-2 PSC Allocations usage utilities Bridges-2: https://www.psc.edu/resources/software/allocations Bridges-2: 1.0
allpathslg Anvil Application Bioinformatics Sciences Biology Allpathslg is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads. https://software.broadinstitute.org/allpaths-lg/blog/ Anvil: https://www.rcac.purdue.edu/software/allpathslg Anvil: 52488
alphafold Aces, Anvil, Darwin, Faster Web Application Prediction Tool Biological Sciences Structural Biology Bioinformatics AlphaFold, the state-of-the-art AI system developed by DeepMind, is able to computationally predict protein structures with unprecedented accuracy and speed.
Description Source: https://alphafold.ebi.ac.uk/about
AlphaFold uses a novel attention-based neural network architecture that interprets the amino acid sequence of a protein and predicts its 3D structure. It leverages evolutionary information from multiple sequence alignments to improve prediction accuracy. The system also provides confidence scores for its predictions. Protein Folding, Structure Prediction, Deep Learning, Neural Networks https://alphafold.ebi.ac.uk/ https://github.com/google-deepmind/alphafold https://github.com/google-deepmind/alphafold?tab=readme-ov-file#installation-and-running-your-first-prediction Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/alphafold
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.3.2-Cuda-11.8.0
Anvil: 2.1.1, 2.2.0, 2.2.3, 2.3.0, 2.3.1
Faster: 2.1.1, 2.2.2-Cuda-11.3.1
AlphaFold is a deep learning-based system developed by DeepMind to predict protein folding and 3D structure with high accuracy.
alphapickle Aces, Faster Data Analysis Library Other Mathematics Quantitative Finance Financial Engineering AlphaPickle is a versatile Python script designed to extract and present output data from DeepMind's ALPHAFOLD protein prediction algorithm, simplifying complex .pkl and .json files into user-friendly formats, alongside generating plots for easier analysis. Automated alpha factor research, portfolio optimization, backtesting, risk management tools, performance analysis, support for common financial data formats. Python Library, Quantitative Finance, Alpha Factors, Portfolio Optimization https://github.com/mattarnoldbio/alphapickle https://github.com/mattarnoldbio/alphapickle Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.4.1
Faster: 1.4.1
Alphapickle is a Python library that provides tools and utilities for working with alpha factors and optimizing portfolio construction in quantitative finance.
alsa-lib Faster Audio Library Library Computer & Information Sciences The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.
Description Source: https://www.alsa-project.org/wiki/Main_Page
1. Allows access to sound card capabilities in Linux
2. Provides audio and MIDI functionality
3. Supports various audio formats
4. Offers low latency audio processing
5. Enables hardware-level audio control
Linux, Audio, Library https://www.alsa-project.org/wiki/Main_Page https://www.alsa-project.org/wiki/Documentation Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.2.8 Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system. alsa-lib is a library that provides an interface for programmers to access sound card capabilities.
amask Stampede3 Molecular Visualization Software Visualization Biological Sciences The amask tool exposes the process masks (affinity) of an application will have in a parallel environment, so that users can determine the cores/hardware-threads where each process is allowed to run. 1. Interactive manipulation of molecular structures
2. Visualization of atomic interactions and bonds
3. Rendering quality images and animations of molecular simulations
4. Support for various file formats commonly used in molecular modeling
5. User-friendly interface for easy navigation and editing
Molecular Visualization, Atomic Structures, Molecular Modeling, Research Tool https://tacc.utexas.edu/research/tacc-research/amask/ https://github.com/TACC/amask https://github.com/TACC/amask/blob/master/README Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Stampede-3: 1.0 Amask is a high-level molecular visualization program that is designed to create and manipulate atomic structures for research and educational purposes. It provides a user-friendly interface for visualizing complex molecular structures and interactions.
amber Anvil, Expanse, Faster Molecular Dynamics Simulation Biological Sciences Biophysics, Structural Biology Biochemistry & Molecular Biology Amber is a suite of biomolecular simulation programs together with Amber tools. 1. Molecular dynamics simulations
2. Free energy calculations
3. Quantum chemistry
4. Structural analysis
5. Visualization tools
Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry https://ambermd.org/ https://ambermd.org/doc12/Amber23.pdf https://ambermd.org/tutorials/ Anvil: https://www.rcac.purdue.edu/software/amber
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 20
Expanse: C6Gwmih-Omp, Ulauqq7-Omp
Faster: 20-Cuda-11.4.1-Nccl-2.11.4-Python-3.9.5, 20-Cuda-11.4.1-Python-3.9.5
Amber is a suite of highly extensible molecular simulation programs. It is designed for simulations of biomolecules such as proteins, nucleic acids, and carbohydrates, and can also be used for small molecules.
ambertools Aces, Faster Simulation Software Software Tools Biological Sciences Structural Biology Biophysics Ambertools is a suite can of complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. AmberTools offers a wide range of functionality for molecular dynamics simulations, including energy minimization, molecular dynamics simulation, structure analysis, and visualization. It supports various force fields and parameters for simulating biomolecules. Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization https://ambermd.org/AmberTools.php https://ambermd.org/doc12/Amber23.pdf https://ambermd.org/tutorials/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 22.3
Faster: 21.12
AmberTools is a suite of software for molecular dynamics simulations, energy minimization, and trajectory analysis in the field of computational chemistry. It provides tools for the refinement and analysis of biomolecular structures.
amd-rocm Darwin Toolkit Environment AMD ROCm is a comprehensive software ecosystem tailored for GPU-accelerated computing tasks, offering robust support for parallel processing and machine learning applications. https://www.amd.com/en/developer/resources/rocm-hub.html https://rocm.docs.amd.com/en/latest/index.html
amd-uprof Darwin Compiler/Profiler Performance Analysis Tool Computer & Information Sciences Software Engineering, Systems, & Development Computer Science AMD uProf (“MICRO-prof”) is a software profiling analysis tool for x86 applications running on Windows, Linux and FreeBSD operating systems and provides event information unique to the AMD “Zen”-based processors and AMD Instinct™ MI Series accelerators. AMD uProf enables the developer to better understand the limiters of application performance and evaluate improvements. 1. Performance analysis tools for AMD processors.
2. Detailed insights into application performance.
3. Power usage analysis.
4. Code optimization capabilities.
5. Identify performance bottlenecks.
Performance Analysis, Application Optimization, Amd Processors https://www.amd.com/en/developer/uprof.html https://www.amd.com/content/dam/amd/en/documents/developer/version-4-2-documents/uprof/uprof-user-guide-v4.2.pdf AMD uProf is a performance analysis tool suite for AMD processors that provides detailed insights into application performance and power usage. It allows developers to analyze code performance, identify bottlenecks, and optimize applications for AMD platforms.
amdblis Anvil, Expanse Computational Tool Data Analysis & Visualization Biological Sciences Single-Molecule Biophysics Biophysics AMD Optimized BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. Amdblis includes tools for data analysis from single-molecule experiments, such as particle tracking, dwell time analysis, and fluorescence analysis. It also offers visualization capabilities for generating plots and heat maps. Computational Software, Data Analysis, Visualization https://www.amd.com/es/developer/aocl/blis.html https://github.com/flame/blis https://github.com/flame/blis Anvil: https://www.rcac.purdue.edu/software/amdblis
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.0
Expanse: Zcuungw-Omp, 6Sfatsa
Amdblis is a computational software for analyzing and visualizing single-molecule data, particularly for biophysical studies.
amdfftw Anvil, Expanse Library Mathematics Engineering Mathematics An AMD optimized version of FFTW. FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.
Description Source: https://www.fftw.org/
https://www.fftw.org/ https://github.com/amd/amd-fftw https://www.fftw.org/fftw3_doc/Tutorial.html Anvil: https://www.rcac.purdue.edu/software/amdfftw
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.0
Expanse: T757St4, Zqoqbjf-Omp, ...
amdlibflame Anvil, Expanse Library Computational Software Computer & Information Sciences Engineering Mathematics libFLAME AMD Optimized version is a portable library for dense matrix computations, providing much of the functionality present in Linear Algebra Package LAPACK. It includes a compatibility layer, FLAPACK, which includes complete LAPACK implementation. High-Performance Implementation Of Dense Linear Algebra Routines On Cpus, Open-Source Nature For Accessibility & Customization, Efficient & Robust Algebraic Computations For Numerical Linear Algebra Applications Linear Algebra, Numerical Computations, Performance Optimization https://www.amd.com/en/developer/aocl/blis.html#AOCL-libflame https://github.com/amd/libflame Anvil: https://www.rcac.purdue.edu/software/amdlibflame
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.0
Expanse: F37Pl2Z
AMD LIBFLAME is an open-source software library that provides a high-performance implementation of the dense linear algebra routines on CPUs. It aims to offer efficient and robust algebraic computations for numerical linear algebra applications.
amdlibm Anvil, Expanse Math Library Library Engineering & Technology Engineering Mathematics AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor-based machines. It provides many routines from the list of standard C99 math functions. Applications can link into AMD LibM library and invoke math functions instead of compilers math functions for better accuracy and performance. Some core features of amdlibm include optimized mathematical functions for common operations such as elementary functions (e.g., sin, cos), exponential and logarithmic functions, and more. The library is optimized to leverage the advanced capabilities of AMD processors to achieve high performance and accurate computation results. Mathematics, Numerical Computation, Math Library https://www.amd.com/de/developer/aocl/libm.html https://github.com/amd/aocl-libm-ose Anvil: https://www.rcac.purdue.edu/software/amdlibm
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.0
Expanse: Uil3Tqx
AMDlibm is a software library provided by AMD that offers mathematical functions specifically optimized for high performance on AMD processors. It provides a collection of mathematical functions designed to exploit the advanced features of AMD processors for enhanced numerical computation.
amdscalapack Anvil, Expanse Library Mathematics Engineering Mathematics ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. It depends on external libraries including BLAS and LAPACK for Linear Algebra computations. https://www.amd.com/de/developer/aocl/scalapack.html https://github.com/amd/aocl-scalapack Anvil: https://www.rcac.purdue.edu/software/amdscalapack
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.0
Expanse: 7Qg2Ts5
amduprof Delta, Expanse Tool Performance Profiler Computer & Information Sciences Artificial Intelligence & Intelligent Systems Computer Science AMD uProf (“MICRO-prof”) is a software profiling analysis tool for x86 applications running on Windows, Linux and FreeBSD operating systems and provides event information unique to the AMD “Zen”-based processors and AMD Instinct™ MI Series accelerators. AMD uProf enables the developer to better understand the limiters of application performance and evaluate improvements. Profiling Opencl Applications, Analyzing Memory Access Patterns, Identifying Kernel Occupancy, Monitoring Compute Unit Utilization Gpu Profiling, Opencl Profiler, Performance Analysis https://www.amd.com/en/developer/uprof.html https://www.amd.com/content/dam/amd/en/documents/developer/uprof-v4.0-gaGA-user-guide.pdf https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/debug_perf.html Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Delta: 3.5, 3.6, 4.0
Expanse: 3.4.475
amduprof is a tool developed for profiling OpenCL applications on AMD GPUs. It provides insights into the performance of OpenCL kernels by analyzing memory access patterns, kernel occupancy, and compute unit utilization.
amos Faster Sequence Assembly Software Bioinformatics Tool Biological Sciences Genomics Genetics The AMOS consortium is committed to the development of open-source whole genome assembly software. DNA Sequence Assembly, Next-Generation Sequencing Data Analysis, Modular & Open-Source Framework, Various Assembly Algorithms Assembly, DNA Sequencing, Bioinformatics http://amos.sourceforge.net https://amos.sourceforge.net/wiki/index.php/AMOS#Documentation https://amos.sourceforge.net/wiki/index.php/Programmer%27s_guide Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.1.0 AMOS (A Modular Open-Source Assembler) is a collection of tools and techniques for assembly of DNA sequences. It includes a robust collection of assembly algorithms and pipeline components for analyzing data from common next-generation sequencing platforms.
amphora2 Faster Computational Software Bioinformatics Tool Biological Sciences Ecology Biological Sciences An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences. 1. Phylogenetic placement of metagenomic reads
2. Taxonomic classification of microbial sequences
3. Accurate estimation of phylogenetic relationships
4. Rapid analysis of complex environmental samples
Bioinformatics, Metagenomics, Phylogenetics https://github.com/wu-lab-uva/AMPHORA2 Faster: https://hprc.tamu.edu/software/faster/ Faster: 20190730-Java-13-Pthreads-Avx2 Amphora2 is a bioinformatics tool designed for the accurate and rapid estimation of phylogenetic placement of metagenomic reads. It facilitates the taxonomic classification of microbial sequences within complex environmental samples.
amptk Anvil Application Bioinformatics Biological Sciences Sciences Biological Sciences Amptk is a series of scripts to process NGS amplicon data using USEARCH and VSEARCH, it can also be used to process any NGS amplicon data and includes databases setup for analysis of fungal ITS, fungal LSU, bacterial 16S, and insect COI amplicons. 1. Demultiplexing and quality filtering of raw sequencing data.
2. Denoising and dereplication of sequences to remove errors.
3. Chimera removal to improve the accuracy of data.
4. OTU picking based on clustering at specified sequence similarities.
5. Taxonomic assignment of OTUs using reference databases.
6. Diversity analyses for comparing microbial communities.
Bioinformatics, Amplicon Analysis, Metabarcoding, High-Throughput Sequencing, 16S Rrna Gene, Its Sequences https://github.com/nextgenusfs/amptk https://amptk.readthedocs.io/en/latest/ Anvil: https://www.rcac.purdue.edu/software/amptk Anvil: 1.5.4 Amplicon analysis and metabarcoding toolkit (amptk) is a bioinformatics pipeline for analyzing high-throughput amplicon sequencing data such as 16S rRNA gene sequences and Internal Transcribed Spacer (ITS) sequences. It provides various modules for processing raw sequence data, including demultiplexing, quality filtering, denoising, chimera removal, operational taxonomic unit (OTU) picking, taxonomic assignment, and diversity analysis.
anaconda Anvil, Darwin, Jetstream, Ookami Package Management Software Development Computer & Information Sciences Informatics, Analytics & Information Science Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. Anaconda includes over 250 popular data science packages and their dependencies such as NumPy, pandas, scipy, scikit-learn, and Jupyter, along with conda package manager for managing virtual environments and deploying packages. Data Science, Scientific Computing, Package Management, Python, R https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Anvil: https://www.rcac.purdue.edu/software/anaconda
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Anvil: 2021.05-Py38
Jetstream: 22.9.0
Ookami: 3
Anaconda is a free and open-source distribution of Python and R programming languages for scientific computing, that aims to simplify package management and deployment.
anaconda2 Bridges-2 Distribution Scientific Computing Computer & Information Sciences, Artificial Intelligence & Intelligent Systems Anaconda is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda. 1. Simplified package management through the conda package manager. 2. Includes a wide range of commonly used scientific computing libraries and tools. 3. Supports Python and R programming languages. 4. Cross-platform compatibility for Windows, macOS, and Linux. 5. Integrated environments such as Jupyter Notebook for interactive computing. Python Libraries, Conda Packages, Data Science, Scientific Computing, Machine Learning, Computational Software Bridges-2: https://www.psc.edu/resources/software/anaconda2 Bridges-2: 2019.10 Anaconda2 is a free and open-source distribution of the Python and R programming languages for scientific computing, that aims to simplify package management and deployment. It includes over 720 open-source packages and is widely used for data science, machine learning, and scientific computing.
anaconda3 Aces, Bridges-2, Expanse, Faster Development Tools Programming Language Distribution Computer & Information Sciences Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. Comprehensive Python Distribution For Scientific Computing, Package Management With Conda Package Manager, Includes Popular Data Science Packages Like Numpy, Pandas, Matplotlib, Etc., Cross-Platform Support, Ability To Create Isolated Environments For Different Projects Python, Data Science, Machine Learning, Deep Learning, Package Management https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Aces: https://hprc.tamu.edu/software/aces/
Bridges-2: https://www.psc.edu/resources/software/anaconda3
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021.11, 2022.05, 2022.10, 2023.03-1, 2023.07-2, 2024.02-1
Bridges-2: 2020.07, 2020.11, 2022.10
Expanse: Kfluefz, Q4Munrg
Faster: 2020.11, 2021.05, 2021.11, 2022.05, 2022.10, 2023.03-1, 2023.07-2, ...
Anaconda is a free and open-source distribution of Python programming language for scientific computing that aims to simplify package management and deployment. It includes over 250 popular data science packages and their dependencies, making it a one-stop solution for Python programming in data science, machine learning, deep learning, and other related fields.
anaconda3_cpu Delta Environment Manager Package Management Computer & Information Sciences Data Science, Scientific Computing, Machine Learning Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. 1. Bundled with a wide range of scientific computing packages and libraries
2. Supports package management and environment creation
3. Includes tools for data science, machine learning, and scientific computing
4. Cross-platform compatibility for Windows, macOS, and Linux
5. Optimized for CPU-based computations
Package Manager, Python Environment, Scientific Computing, Data Science, Machine Learning https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 23.3.1, 23.7.4 Anaconda is a popular package and environment manager for Python and R programming languages. Anaconda3 specifically refers to the Python 3 version of Anaconda, which includes a wide range of pre-installed scientific computing packages and libraries. The CPU version indicates that it is optimized for central processing unit (CPU) computations.
anaconda3_gpu Delta Application Python And R Repo Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 22.10.0, 23.3.1, ...
anaconda3_mi100 Delta Application Python And R Repo Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 4.14.0, 23.7.4
anaconda3_rcpu Delta Application Python And R Repo Anaconda3 is a popular open-source distribution of Python and R for scientific computing, data science, and machine learning. It simplifies package management and deployment by bundling numerous libraries and tools, and it includes the conda package manager, which makes installing, running, and updating various packages and their dependencies convenient. https://www.anaconda.com/ https://docs.anaconda.com/index.html https://docs.anaconda.com/free/anaconda/getting-started/
https://www.youtube.com/watch?v=YJC6ldI3hWk
https://www.datacamp.com/tutorial/installing-anaconda-mac-os-x
https://docs.anaconda.com/ae-notebooks/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 22.9.0
anaconda3_x86_64 Delta Distribution Package Manager Other Computer & Information Sciences 1. Simplified package management through conda package manager. 2. Includes popular data science and machine learning libraries like Numpy, Pandas, Scikit-learn, TensorFlow, etc. 3. Enables easy creation of virtual environments for different projects. 4. Jupyter notebook integration for interactive coding and data visualization. 5. Supports Windows, macOS, and Linux platforms. Software Distribution, Scientific Computing, Data Science, Machine Learning Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 23.3.1, 23.7.4 Anaconda is a free, open-source distribution of Python and R programming languages for scientific computing, that aims to simplify package management and deployment. It includes hundreds of popular data science, machine learning, and scientific computing packages.
ananse Anvil Tool Data Analysis Other Natural Sciences Sciences Biological Sciences ANANSE is a computational approach to infer enhancer-based gene regulatory networks (GRNs) and to identify key transcription factors between two GRNs. Ananse offers functionalities for network visualization, analysis, and manipulation. It supports various network types, such as protein-protein interaction networks, gene regulatory networks, and metabolic networks. Users can apply different algorithms for network analysis, clustering, and identifying important network nodes. The tool also provides interactive visualization options for exploring network properties. Network Analysis, Visualization, Biological Networks https://github.com/vanheeringen-lab/ANANSE https://anansepy.readthedocs.io/en/master/ https://anansepy.readthedocs.io/en/master/examples/ Anvil: https://www.rcac.purdue.edu/software/ananse Anvil: 0.4.0 Ananse is a software tool used for analyzing and visualizing network structures, including complex biological networks.
anchorwave Anvil Computational Tool Prediction Tool Biological Sciences Biophysics Bioinformatics Anchorwave is used for sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism and whole-genome duplication variation. Prediction Of RNA Secondary Structures, Calculation Of Minimum Free Energy Structures, Utilizes Statistical Thermodynamics, Incorporates Dynamic Programming Algorithms Computational Software, Bioinformatics, RNA Secondary Structures, Thermodynamics, Dynamic Programming https://github.com/baoxingsong/AnchorWave https://github.com/baoxingsong/AnchorWave https://github.com/baoxingsong/AnchorWave?tab=readme-ov-file#example Anvil: https://www.rcac.purdue.edu/software/anchorwave Anvil: 1.0.1, 1.1.1 AnchorWave is a computational software for the analysis and prediction of RNA secondary structures. It uses statistical thermodynamics and dynamic programming algorithms to calculate the minimum free energy structure of RNA sequences.
angsd Anvil, Faster Application Bioinformatics Biological Sciences Sciences Biology Angsd is a software for analyzing next generation sequencing data. Some core features of angsd include genotype likelihood estimation, mapping quality control, allele frequency estimation, phylogenetic analysis, and population genetic analysis. Ngs Data Analysis, Genome-Wide Association Studies, Population Genomics, Genetic Variation https://github.com/ANGSD/angsd https://www.popgen.dk/angsd/index.php/ANGSD https://www.popgen.dk/angsd/index.php/Quick_Start Anvil: https://www.rcac.purdue.edu/software/angsd
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 0.935, 0.937, 0.939, 0.940
Faster: 0.935
angsd is a software for analyzing Next Generation Sequencing (NGS) data such as genome-wide association studies (GWAS) and population genomics data.
annogesic Anvil Tool Bioinformatics Biological Sciences Genetics Biological Sciences ANNOgesic is the swiss army knife for RNA-Seq based annotation of bacterial/archaeal genomes. Identification Of Transcription Start Sites (Tsss), Prediction Of Operon Structures, Detection Of Small RNAs, Analysis Of RNA-RNA Interactions, Identification Of RNA Motifs RNA-Seq Analysis, Bacterial Genomes, Transcription Start Sites, Operon Structures, Small RNAs, RNA Motifs, RNA-RNA Interactions https://github.com/Sung-Huan/ANNOgesic https://annogesic.readthedocs.io/en/latest/index.html https://annogesic.readthedocs.io/en/latest/tutorial.html Anvil: https://www.rcac.purdue.edu/software/annogesic Anvil: 1.1.0 ANNOgesic is a software tool designed to analyze RNA-seq data for the identification of various elements in bacterial genomes. It integrates multiple steps of RNA-seq analysis to predict transcription start sites (TSSs), operon structures, small RNAs, RNA-RNA interactions, and RNA motifs.
annovar Anvil Bioinformatics Tool Genomic Annotation Tool Biological Sciences Sciences Biology ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). Variant Annotation, Gene-Based Annotations, Functional Prediction, Prioritize Variants, Population Frequencies, Conservation Scores Genomics, Genetic Variation, Bioinformatics, Annotation https://annovar.openbioinformatics.org/en/latest/ https://annovar.openbioinformatics.org/en/latest/ https://annovar.openbioinformatics.org/en/latest/user-guide/startup/ Anvil: https://www.rcac.purdue.edu/software/annovar Anvil: 2022-01-13 ANNOVAR is a powerful software tool designed to annotate genetic variants detected from diverse genomes.
ansys Bridges-2, Faster Engineering Simulation Software Simulation Software Engineering & Technology Engineering Mechanical Engineering ANSYS is an engineering simulation software used for testing and predicting the behavior of components and systems in various fields. It offers tools for finite element analysis (FEA), computational fluid dynamics (CFD), and other multiphysics simulations, enabling engineers to analyze performance, durability, and fluid dynamics under real-world conditions. Key features of Ansys include structural analysis, computational fluid dynamics (CFD), explicit dynamics, multiphysics, electronics thermal management, and additive manufacturing simulation. Engineering, Simulation, Product Design https://www.ansys.com/ Bridges-2: https://www.psc.edu/resources/software/ansys
Faster: https://hprc.tamu.edu/software/faster/
Bridges-2: 201, 212, 221, 222
Faster: 2022R2
Stampede-3: 24.1
Ansys provides engineering simulation software used to predict how product designs will behave and how manufacturing processes will operate in real-world environments. The software enables engineers to simulate interactions of all disciplines like structural, fluids, heat transfer, electromagnetic, and systems engineering.
ant Aces, Expanse, Faster Tool Build Automation Computer Science Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. Ant supplies a number of built-in tasks allowing to compile, assemble, test and run Java applications.
Description Source: https://ant.apache.org/
Ant provides a simple XML-based build file that outlines the steps needed to build a project. It facilitates the compilation of Java code, running tests, packaging applications, and deploying them. Ant is extensible and can be integrated with other tools and libraries. Automation, Java, Build Tool, Deployment https://ant.apache.org/ https://ant.apache.org/manual/ https://www.tutorialspoint.com/ant/ant_quick_guide.htm
https://www.vogella.com/tutorials/ApacheAnt/article.html
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.10.11-Java-11, 1.10.12-Java-11
Expanse: Hcgc7Fk, 5Soub24
Faster: 1.10.5-Java-1.8, 1.10.9-Java-11, 1.10.11-Java-11, 1.10.12-Java-11
Ant is a build automation tool that is mainly used for Java projects. It automates the process of compiling and building Java applications, along with tasks such as testing and deployment.
antismash Anvil Annotation Tool Genomics & Bioinformatics Tools Biological Sciences Genomics Bioinformatics Antismash allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. Detection & Annotation Of Gene Clusters Involved In Secondary Metabolite Production, Prediction Of Putative Functions Of Biosynthetic Enzymes, Identification Of Potential Bioactive Compounds & Natural Products, Visualization Of Gene Clusters & Biosynthetic Pathways, Integration Of Multiple Bioinformatics Tools & Databases Bioinformatics, Genome Mining, Biosynthetic Gene Clusters, Secondary Metabolites https://docs.antismash.secondarymetabolites.org/ https://docs.antismash.secondarymetabolites.org/ Anvil: https://www.rcac.purdue.edu/software/antismash Anvil: 5.1.2, 6.0.1, 6.1.0 AntiSMASH is a comprehensive software tool for the automatic genome mining, analysis, and annotation of biosynthetic gene clusters (BGCs) in microbial genomes. It is widely used in bioinformatics and drug discovery research to identify and characterize secondary metabolite biosynthesis pathways.
antlr Aces, Faster Toolkit Compilers ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.
Description Source: https://www.antlr.org/
Powerful Parser Generator, Support For Multiple Programming Languages, Parsing Expression Grammar (Peg) Support, Automatic Ast Construction, Lexer & Parser Generation Compiler, Parser Generator, Syntax Analysis, Code Generation https://www.antlr.org/ https://www.antlr.org/api/ https://tomassetti.me/antlr-mega-tutorial/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.7.7-Java-11
Faster: 2.7.7-Java-11
ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.
anvio Anvil, Bridges-2 Bioinformatics Tool Analysis & Visualization Platform Biological Sciences Microbiome Research Biological Sciences Anvio is an analysis and visualization platform for 'omics data. Some core features of Anvi'o include metagenomic binning, interactive data exploration, genome assembly visualization, multi-omics integration, and phylogenetic profiling. Omics Data Analysis, Microbiome, Metagenomics, Bioinformatics https://anvio.org/ https://github.com/merenlab/anvio https://anvio.org/learn/ Anvil: https://www.rcac.purdue.edu/software/anvio
Bridges-2: https://www.psc.edu/resources/software/anvio
Anvil: 7.0, 7.1_Main, 7.1_Structure
Bridges-2: 7
Anvi'o is an analysis and visualization platform for omics data. It is designed to help researchers explore complex microbial datasets and perform various tasks such as binning, genome assembly, metagenomic analysis, and visualization.
any2fasta Anvil, Faster Bioinformatics Tool Data Conversion Natural Sciences Genetics Biological Sciences Any2fasta can convert various sequence formats to FASTA. 1. Convert sequence data to FASTA format
2. Support for DNA, RNA, protein sequences
3. Compatible with a variety of sequence data formats
4. Simple and user-friendly interface for quick conversions
Sequence Data, Fasta Format, Bioinformatics https://github.com/tseemann/any2fasta https://github.com/tseemann/any2fasta https://github.com/tseemann/any2fasta?tab=readme-ov-file#examples Anvil: https://www.rcac.purdue.edu/software/any2fasta
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 0.4.2
Faster: 0.4.2
any2fasta is a tool for converting sequence data in various formats to the standard FASTA format. It allows users to easily convert DNA, RNA, protein sequences, and other biological sequence data into the FASTA format for compatibility with a wide range of bioinformatics tools and databases.
aocc Aces, Anvil, Bridges-2, Delta, Expanse, Faster, Ookami Service Compiler Computer & Information Sciences AOCC a set of production compilers optimized for software performance when running on AMD host processors using the AMD “Zen” core architecture.The AOCC compiler environment simplifies and accelerates development and tuning for x86 applications built with C, C++, and Fortran languages.
Description Source: https://www.amd.com/en/developer/aocc.html
AOCC is designed to provide high performance on AMD processors by leveraging advanced optimizations and features specific to AMD architectures. It offers enhanced vectorization, link-time optimization, and improved code generation. Compiler, C, C++, Fortran, Optimization https://www.amd.com/en/developer/aocc.html https://www.amd.com/content/dam/amd/en/documents/developer/version-4-1-documents/aocc/aocc-4.1-user-guide.pdf Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/aocc
Bridges-2: https://www.psc.edu/resources/software/aocc
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 4.0.0
Anvil: 3.1.0
Bridges-2: 2.2.0, 2.3.0
Delta: 4.1.0
Expanse: Io3S466
Faster: 3.1.0
Jetstream: Aocc-Compiler-4.0.0
Ookami: 3.0.0
The AMD Optimizing C/C++ Compiler (AOCC) is a high performance compiler suite with support for C, C++, and Fortran programming languages.
aocc compiler Jetstream Compilers Compiler Computer & Information Sciences AOCC a set of production compilers optimized for software performance when running on AMD host processors using the AMD “Zen” core architecture.The AOCC compiler environment simplifies and accelerates development and tuning for x86 applications built with C, C++, and Fortran languages.
Description Source: https://www.amd.com/en/developer/aocc.html
Support For The Latest C & C++ Standards, Advanced Optimization Features For Amd Processors, Built Upon The Open64 Compiler Infrastructure Compiler, C/C++, Optimization, Amd https://www.amd.com/en/developer/aocc.html https://www.amd.com/content/dam/amd/en/documents/developer/version-4-1-documents/aocc/aocc-4.1-user-guide.pdf The AMD Optimizing C/C++ Compiler is a high performance compiler suite that builds upon the Open64 compiler infrastructure. It includes support for the latest C and C++ standards, as well as numerous advanced optimization features for AMD processors.
aocl Bridges-2, Darwin Compiler Development Tools Engineering & Technology Engineering Mathematics AOCL is a set of numerical libraries optimized for AMD processors based on the AMD “Zen” core architecture and generations. The tuned implementations of industry-standard math libraries enable rapid development of scientific and high-performance computing applications.
Description Source: https://www.amd.com/en/developer/aocl.html
1. Allows developers to target Intel FPGAs for acceleration.
2. Supports OpenCL for FPGA programming.
3. Provides optimization tools for FPGA design.
4. Enables developers to harness the parallel processing power of FPGAs.
5. Facilitates high-performance computing through FPGA acceleration.
Fpga, Opencl, Acceleration https://www.amd.com/en/developer/aocl.html https://www.amd.com/content/dam/amd/en/documents/developer/version-4-1-documents/aocl/aocl-4-1-user-guide.pdf Bridges-2: https://www.psc.edu/resources/software/aocl Bridges-2: 3.1.0 The Intel FPGA SDK for OpenCL (aocl) is a software development kit that allows developers to create high-performance FPGA-accelerated applications using OpenCL. It provides a framework for FPGA programming with OpenCL, enabling developers to leverage the parallel processing capabilities of FPGAs for accelerating their applications.
aocl-sparse Expanse Library Compiler/Tool Engineering & Technology Engineering Mathematics AOCL-Sparse contains basic linear algebra subroutines for sparse matrices and vectors optimized for AMD processors. In addition, AOCL-Sparse includes iterative sparse solvers for solving linear system of equations. It is designed to be used with C and C++. Optimizes Sparse Matrix Operations On Fpgas, Supports Custom Sparse Matrix Kernels Development, Integration With Opencl Applications For Hpc, Enhanced Performance For Sparse Matrix Computations Sparse Matrix Operations, Fpga Optimization, Opencl Applications, High-Performance Computing https://www.amd.com/en/developer/aocl/sparse.html https://github.com/amd/aocl-sparse Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Fg4Cxoj The aocl-sparse tool is part of the Intel FPGA SDK for OpenCL and is designed for optimizing sparse matrix operations on FPGAs. It provides a framework for developing custom sparse matrix kernels and integrating them into OpenCL applications for high-performance computing.
apptainer Jetstream Development Software Tools Engineering & Technology Apptainer, formerly known as Singularity, is an open-source container platform designed to create portable and reproducible environments for scientific computing. It allows users to package applications, their dependencies, and data in a single container that can be run consistently across different computing environments.
Description Source: https://apptainer.org/
Creation & Management Of Containerized Applications, User-Friendly Interface, Packaging, Distribution, & Deployment Of Applications, Support For Containerization Technology, Simplified Application Lifecycle Management Containerization, Application Management, Devops, Software Development https://apptainer.org/ https://apptainer.org/documentation/ https://apptainer.org/docs/user/main/quick_start.html Jetstream: 1.1.6 Apptainer is a tool for creating and managing containerized applications in a simplified and efficient manner. It provides a user-friendly interface for developers and system administrators to package, distribute, and deploy applications using containerization technology.
apr Aces, Faster Development Library Engineering & Technology APR (Apache Portable Runtime) is a library that provides a set of APIs designed to abstract away the details of the operating system, thereby offering a consistent interface for programming tasks across different platforms. It facilitates the development of portable applications by providing a standardized set of functions for network communication, file system access, and other system utilities, enhancing portability and reducing the complexity of handling OS-specific differences. APR provides a set of APIs that abstract many operating system-specific functionalities, such as file I/O, networking, threading, and inter-process communication. It aims to simplify the development of cross-platform applications by providing a common API for various operating system functions. Software Library, Cross-Platform Development, Operating System Abstraction https://apr.apache.org/ https://apr.apache.org/docs/apr/1.7/modules.html https://people.apache.org/~rooneg/talks/portable-c-with-apr/apr.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.7.0
Faster: 1.7.0
The Apache Portable Runtime (APR) is a software library that provides a predictable and consistent interface to underlying platform-specific implementations.
apr-util Aces, Faster Library APR-util is a companion library to the Apache Portable Runtime (APR) that provides a set of additional utilities and interfaces for tasks such as database connectivity, XML parsing, and data structures management. It extends the core functionality of APR, offering developers a broader set of tools for building highly portable and scalable applications across different platforms. Database & Sql Support, Ldap (Lightweight Directory Access Protocol) Support, Resource Pooling, Xml Parsing, Uri Parsing, Memory Allocation & Management Utility Library, Apache Portable Runtime, Support Library, Additional Features https://apr.apache.org/ https://apr.apache.org/docs/apr-util/1.6/modules.html https://www.linuxfromscratch.org/blfs/view/svn/general/apr-util.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.6.1
Faster: 1.6.1
Apache Portable Runtime Utility Library (APR-util) provides a set of utility functions to support the Apache Portable Runtime core functionalities. It is a companion library to APR, extending the basic functionality of APR with additional features.
arcade-learning-environment Faster Framework Developer Support Computer Science Artificial Intelligence The Arcade Learning Environment (ALE) is a simple framework that allows researchers and hobbyists to develop AI agents for Atari 2600 games. It is built on top of the Atari 2600 emulator Stella and separates the details of emulation from agent design. This video depicts over 50 games currently supported in the ALE. https://github.com/Farama-Foundation/Arcade-Learning-Environment https://github.com/Farama-Foundation/Arcade-Learning-Environment/blob/master/docs/README.md Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.7.3, 0.8.1
archive-zip Faster Application Provides an interface to ZIP archive files. Creating Zip Archives, Reading Zip Archives, Extracting Files & Directories, Compression & Decompression Using Zip Format Python Library, Zip Archives, Compression, Decompression https://metacpan.org/pod/Archive::Zip https://metacpan.org/pod/Archive::Zip Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.68 archive-zip is a simple, easy-to-use Python library for creating, reading, and extracting ZIP archives. It provides functionality to compress and decompress files and directories using the ZIP format.
archspec Aces, Faster Framework Software Development Computer & Information Sciences Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them.
Description Source: https://github.com/archspec/archspec
Detecting System Architecture, Producing Structured Representation Of System Features, Performance Optimization, Code Generation Architecture Detection, System Analysis, Performance Optimization, Code Generation https://github.com/archspec/archspec https://archspec.readthedocs.io/en/latest/ https://archspec.readthedocs.io/en/latest/getting_started.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.1.2, 0.1.3, 0.1.4, 0.2.0
Faster: 0.1.0-Python-3.8.2, 0.1.0-Python-3.8.6, 0.1.3
Archspec is a framework for detecting the architecture of a system and producing a structured representation of its features for further analysis and optimization. It aims to provide insights into the architectural characteristics of a computing system, helping developers understand and leverage these features for performance optimization and code generation.
arcs Anvil Research Software Tools & Platforms Engineering & Technology Sciences Biology ARCS is a tool for scaffolding genome sequence assemblies using linked or long read sequencing data. High-Performance Computing Services, Advanced Computational Workflows, Support For Complex Simulations, Data Analysis Capabilities Hpc, Computational Workflows, Data Analysis https://github.com/bcgsc/arcs https://github.com/bcgsc/arcs Anvil: https://www.rcac.purdue.edu/software/arcs Anvil: 1.2.4 ARCS (Advanced Research Computing Services) is a software platform developed to provide high-performance computing (HPC) services to researchers in various fields. It aims to enhance computational workflows and facilitate complex simulations and data analysis.
aria2 Expanse, Faster Download Manager Utility Computer & Information Sciences, Other Computer & Information Sciences aria2 is a utility for downloading files. The supported protocols are HTTP(S), FTP, SFTP, BitTorrent, and Metalink. aria2 can download a file from multiple sources/protocols and tries to utilize your maximum download bandwidth.
Description Source: https://aria2.github.io/manual/en/html/aria2c.html
Multi-Protocol & Multi-Source Command-Line Download Utility, Supports Http/Https, Ftp, Sftp, Bittorrent, Metalink, Configurable Download Settings, Batch Downloading, Download Resuming, Parallel Downloads Download Manager, Command-Line Tool, Multi-Protocol, Multi-Source, File Transfer https://aria2.github.io/ https://aria2.github.io/manual/en/html/aria2c.html https://aria2.github.io/manual/en/html/aria2c.html#example Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Expanse: D7R7Iaa, Q32Jtg2
Faster: 1.35.0
aria2 is a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
aria2-1.15.1 Faster Faster: https://hprc.tamu.edu/software/faster/
ariba Anvil Cloud-Based Software Procurement Sciences Biology ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. Automated Procurement Processes, Supplier Management, Sourcing Capabilities, Contract Management, Spend Analysis Tools Procurement Software, Cloud-Based Solution, Source-To-Pay Process Management https://sanger-pathogens.github.io/ariba/ https://github.com/sanger-pathogens/ariba https://github.com/sanger-pathogens/pathogen-informatics-training Anvil: https://www.rcac.purdue.edu/software/ariba Anvil: 2.14.6 Ariba is a cloud-based procurement software solution designed to help businesses manage their entire source-to-pay process more efficiently and effectively. It offers a range of modules for procurement, sourcing, contract management, supplier management, and spend analysis.
arm Ookami Compiler/Debugger Development Tools Engineering & Technology Electrical, Electronic, & Information Engineering Engineering & Technology The Arm architecture serves as the foundation for processors, known as Processing Elements (PE). It enables interoperability across diverse Arm devices, facilitating software development and execution. Arm compiler, Arm debugger, Arm profiler, Code optimization, Debugging tools, Performance analysis tools Software Development, Embedded Applications, Debugging, Performance Optimization https://developer.arm.com/ https://developer.arm.com/documentation/ https://learn.arm.com/?icid=devhub:developer:all-pages:nav-link Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: Forge/22.1.1 Arm is a software development suite for building and debugging embedded applications on Arm-based devices. It provides tools for optimizing code for performance, debugging, and profiling applications for a wide range of Arm processors.
arm-forge Expanse Toolkit Arm Forge integrates Arm DDT for parallel debugging, Arm MAP for performance profiling, and Arm Performance Reports for summarizing application performance, supporting various parallel architectures like MPI, CUDA, and OpenMP. https://developer.arm.com/ https://developer.arm.com/documentation/101136/22-1-3/Arm-Forge/Introduction-to-Arm-Forge https://developer.arm.com/documentation/101136/22-1-3/Arm-Forge/Introduction-to-Arm-Forge/Online-resources Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 21.0.1-Linux-X86_64
arm-gnu-toolchain Aces Compiler Development Tool Engineering & Technology The GNU Toolchain for the Arm Architecture releases produced by Arm (referred to as “Arm GNU Toolchain”) enable partners, developers and the community to use new features from recent Arm Architecture and from open-source projects GCC, Binutils, glibc, Newlib, and GDB. Support For Compiling C/C++ Code For Arm Processors, Assembly Language Support, Highly Optimized Code Generation For Embedded Systems, Debugging Capabilities With Gdb, Open-Source Tools With Strong Community Support Compiler, Embedded Systems, Arm Processor, Toolchain https://developer.arm.com/ https://developer.arm.com/Tools%20and%20Software/GNU%20Toolchain https://developer.arm.com/documentation/ka005946/1-0/?lang=en Aces: https://hprc.tamu.edu/software/aces/ Aces: 12.3 The ARM GNU Toolchain is a collection of tools/libraries used to create applications for embedded ARM processors. It includes the GNU Compiler Collection (GCC) for compiling C/C++ code, GNU Binutils for creating/executing binary files, and GDB for debugging.
arm-gnu-toolchaint Aces Aces: https://hprc.tamu.edu/software/aces/ Aces: 12.3
armadillo Aces, Delta, Expanse, Faster Linear Algebra Library Library Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Armadillo is a high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use. It provides high-level syntax and functionality deliberately similar to Matlab.
Description Source: https://arma.sourceforge.net/
1. Fast matrix operations including decomposition, factorization, and vectorization.
2. Seamless integration with C++ programming.
3. Various advanced features such as sparse matrices, expression templates, and delayed evaluation.
4. Extensive documentation and examples for users' convenience.
5. Portable and compatible with various operating systems.
Linear Algebra, C++ Library https://arma.sourceforge.net/ https://arma.sourceforge.net/docs.html https://arma.sourceforge.net/docs.html#example_prog Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 11.4.3, 12.6.2
Delta: 12.4.0
Expanse: 9.800.3-Openblas
Faster: 10.7.5, 11.4.3, 12.6.2
Armadillo is a high-quality linear algebra library for the C++ programming language. It aims to provide efficient and easy-to-use classes for common linear algebra operations, with a particular focus on real and complex matrices and vectors.
arpack Darwin, Stampede3 Library Numerical Library Mathematics Numerical Analysis Applied Mathematics ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. (This library is no longer maintained)
Description Source: https://lacsi.rice.edu/software/arpak/default.htm
1. Solving large scale eigenvalue problems
2. Ability to handle complex, real, symmetric, and nonsymmetric eigenvalue problems
3. High performance and efficiency
4. Available subroutines for integration into various computational environments
Computational Software, Linear Algebra, Eigenvalue Problems https://github.com/inducer/arpack http://li.mit.edu/Archive/Activities/Archive/CourseWork/Ju_Li/MITCourses/18.335/Doc/ARPACK/Lehoucq97.pdf https://github.com/inducer/arpack/tree/master/EXAMPLES Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Stampede-3: 3.9.1 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. It is capable of solving complex, real, symmetric, and nonsymmetric eigenvalue problems across different fields of scientific computing.
arpack-ng Aces, Anvil, Expanse, Faster Library Mathematics Physical Sciences Mathematics ARPACK-NG is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. ARPACK-NG provides efficient and scalable algorithms for solving large sparse eigenvalue problems, including those arising from applications in physics, chemistry, engineering, and other fields. It supports iterative methods like Arnoldi iteration for computing a few eigenvalues/vectors of a large sparse matrix, with options for finding either the largest or smallest eigenvalues. Linear-Algebra, Eigenvalue Problems, Sparse Matrices, Iterative Methods, Computational Physics, Computational Chemistry, Fortran https://github.com/opencollab/arpack-ng https://github.com/opencollab/arpack-ng/tree/master/DOCUMENTS https://github.com/opencollab/arpack-ng/tree/master/PARPACK/EXAMPLES Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/arpack-ng
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.8.0, 3.9.0
Anvil: 3.8.0
Expanse: Bbylirn, Ccwydfp, ...
Faster: 3.8.0, 3.9.0
ARPACK (ARnoldi PACKage) is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The ARPACK-ng project is a re-implementation of the original ARPACK with the goal of improving its usability, maintainability, and performance across a wide range of modern hardware platforms.
arrayfire Expanse Library Library Computer & Information Sciences Engineering Parallel Computing ArrayFire is a high performance software library for parallel computing with an easy-to-use API. Its array based function set makes parallel programming more accessible. Gpu Acceleration, Parallel Computing, Linear Algebra Operations, Signal Processing, Image Processing, Statistics Software Library, Parallel Computing, Gpu Acceleration, Linear Algebra, Signal Processing, Image Processing, Statistics https://arrayfire.org/docs/index.htm#gsc.tab=0 https://arrayfire.org/docs/index.htm#gsc.tab=0 https://arrayfire.org/docs/examples.htm#gsc.tab=0 Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Pl6Gadm ArrayFire is a high-performance software library for parallel computing with an emphasis on GPU acceleration. It provides a broad range of functionality for accelerated computing, including linear algebra, signal processing, statistics, and image processing.
arriba Bridges-2 Tool Bioinformatics Biological Sciences Transcriptomics Genomics Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting.
Description Source: https://github.com/suhrig/arriba
1. Gene fusion detection in RNA-Seq data
2. Identification of gene fusions, transcript fusions, and fusion transcript isoforms
3. Detailed structural information on detected fusions
4. Fast and accurate analysis
5. Supports multiple input file formats
Software, Gene Fusion Detection, RNA-Seq, Transcriptome Analysis https://github.com/suhrig/arriba https://arriba.readthedocs.io/en/latest/ https://hpc.nih.gov/apps/arriba.html Bridges-2: https://www.psc.edu/resources/software/arriba Bridges-2: 2.3.0 Arriba is a fast and accurate tool for gene fusion detection in RNA-Seq data. It can identify gene fusions, transcript fusions, and fusion transcript isoforms, providing detailed information on their structure.
arrow Aces, Faster Development Platform Data Processing Computer & Information Sciences Computer Science Memory Efficiency Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. Cross-Language Development Platform, Columnar Memory Format, Language-Independent, Efficient Analytic Operations, Support For Modern Hardware Like Cpus & Gpus Data Processing, Data Analytics, In-Memory Data, Standardized Format https://arrow.apache.org/ https://arrow.apache.org/docs/ https://arrow.apache.org/cookbook/cpp/
https://arrow.apache.org/cookbook/java/
https://arrow.apache.org/cookbook/py/
https://arrow.apache.org/cookbook/r/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.0.0, 11.0.0
Faster: 0.17.1, 6.0.0, 8.0.0
Arrow is a cross-language development platform for in-memory data that specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware like CPUs and GPUs.
arrow-r Faster Statistical Software Data Analysis & Visualization Mathematics Statistical Analysis Statistics & Probability R interface to the Apache Arrow C++ library 1. Comprehensive statistical analysis tools
2. Advanced data visualization capabilities
3. Extensive libraries for statistical modeling
4. Integration with R programming language
5. Support for custom functions and packages
6. Interactive graphics and plots
Statistical Computing, Data Visualization, Statistical Modeling, R Programming https://arrow.apache.org/ https://arrow.apache.org/docs/ https://arrow.apache.org/cookbook/cpp/
https://arrow.apache.org/cookbook/java/
https://arrow.apache.org/cookbook/py/
https://arrow.apache.org/cookbook/r/
Faster: https://hprc.tamu.edu/software/faster/ Faster: 6.0.0.2-R-4.1.2, 8.0.0-R-4.2.1 Arrow-R is an open-source statistical computing and graphics software program based on the R programming language. It provides advanced statistical analysis, data visualization, and modeling capabilities for researchers and statisticians.
arviz Faster Python Library Data Analysis & Visualization Other Mathematics Bayesian Statistics Statistics & Probability ArviZ is a Python package for exploratory analysis of Bayesian models. It includes functions for posterior analysis, data storage, model checking, comparison and diagnostics. 1. Visualization of posterior distributions, traces, and diagnostics
2. Summary statistics for posterior samples
3. Probability density plots and pair plots for correlations
4. Comparison of multiple models
5. Goodness-of-fit checks and convergence diagnostics
Python Library, Bayesian Inference, Data Visualization https://github.com/arviz-devs/arviz https://python.arviz.org/en/latest/index.html https://python.arviz.org/en/latest/examples/index.html Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.11.4 ArviZ is a Python package for exploratory analysis of Bayesian models. It provides a common data structure and functions for visualizing and summarizing outputs from Bayesian inference.
ascatngs Anvil Computational Bioinformatics Biological Sciences Genetics Biological Sciences AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing. Generation of allele-specific copy number and ploidy profiles from next-generation sequencing (NGS) data using Allele-Specific Copy number Analysis of Tumors (ASCAT) algorithm in R. Copy Number Analysis, Ploidy Profiles, Ngs Data Analysis https://github.com/cancerit/ascatNgs https://github.com/cancerit/ascatNgs Anvil: https://www.rcac.purdue.edu/software/ascatngs Anvil: 4.5.0 ASCA-based copy number and ploidy profiles for NGS data in R
asciinema Bridges-2 Terminal Recorder Development Tool Computer & Information Sciences asciinema is a suite of tools for recording, replaying, and sharing terminal sessions.
Description Source: https://docs.asciinema.org/
Record Terminal Sessions, Share Recordings On The Web, Playback Recordings In A Terminal Emulator, Built-In Asciinema Player For Playback, Free & Open-Source Terminal Recording, Web Sharing, Cli Tool https://asciinema.org/ https://docs.asciinema.org/ https://docs.asciinema.org/getting-started/ Bridges-2: https://www.psc.edu/resources/software/asciinema Bridges-2: 2.0.2, 2.1.0 asciinema is a free and open-source solution for recording terminal sessions and sharing them on the web. It allows users to record their terminal sessions and playback the recordings directly in a terminal emulator.
ase Aces, Faster Tool Simulation & Modeling Other Natural Sciences Sciences Chemistry ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
Description Source: https://wiki.fysik.dtu.dk/ase/index.html
ASE provides interfaces to a wide range of electronic structure codes like VASP, LAMMPS, Quantum ESPRESSO, and more. It offers support for different file formats, offers tools for symmetry operations, molecule visualization, and analysis of simulation results. Computational Software, Python Library, Molecular Simulations https://wiki.fysik.dtu.dk/ase/ https://wiki.fysik.dtu.dk/ase/ase/ase.html https://wiki.fysik.dtu.dk/ase/tutorials/tutorials.html#tutorials Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.20.1, 3.22.1
Faster: 3.20.1
Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations.
asgal Anvil Alignment & Variant Calling Bioinformatics Tools Biological Sciences Sciences Biology ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. Read Alignment Against Reference Genome, Bam File Generation, Snp Calling, Vcf File Creation Genomics, Bioinformatics, Sequence Analysis https://asgal.algolab.eu/ https://asgal.algolab.eu/documentation https://asgal.algolab.eu/documentation#example Anvil: https://www.rcac.purdue.edu/software/asgal Anvil: 1.1.7 asgal is a lightweight tool that aligns sequencing reads against a reference genome, generating BAM files, calling SNPs, and creating variant call format (VCF) files. It is designed for usability and simplicity in analyzing large genomic datasets.
aspera-connect Anvil, Bridges-2 Application Data Transfer Tool IBM Aspera Connect is an install-on-demand application that facilitates high-speed uploads and downloads with an Aspera transfer server.
Description Source: https://www.ibm.com/docs/en/aspera-connect/4.1?topic=aspera-connect-user-guide-linux
https://www.ibm.com/aspera/connect/ https://www.ibm.com/docs/en/aspera-connect/4.1?topic=aspera-connect-user-guide-linux https://www.ibm.com/docs/en/aspera-connect/4.2?topic=linux-setting-up-connect Anvil: https://www.rcac.purdue.edu/software/aspera-connect
Bridges-2: https://www.psc.edu/resources/software/aspera-connect
Anvil: 4.2.6
Bridges-2: 3.11.0.5
assembly-stats Anvil Stand-Alone Tool Bioinformatics Tool Biological Sciences Sciences Biology Assembly-stats is a tool to get assembly statistics from FASTA and FASTQ files. - Calculates basic statistics on genome assemblies
- Provides information on contig and scaffold lengths
- Calculates NG(x) statistics
- Evaluates basic completeness metrics
Genome Assembly, Bioinformatics https://github.com/sanger-pathogens/assembly-stats https://github.com/sanger-pathogens/assembly-stats https://github.com/sanger-pathogens/assembly-stats?tab=readme-ov-file#example Anvil: https://www.rcac.purdue.edu/software/assembly-stats Anvil: 1.0.1 assembly-stats is a tool for summary statistics of genome assembly, providing information on contig and scaffold lengths, NG(x) statistics, and basic completeness metrics.
assimp Aces 3D Modeling/Rendering Library Computer & Information Sciences Computer Science File Loading Open Asset Import Library is a library to load various 3d file formats into a shared, in-memory imediate format. It supports more than 40 file formats for import and a growing selection of file formats for export.
Description Source: https://assimp.org/
1. Import support for multiple 3D model formats. 2. Export support for 3D files. 3. Offers a C++ interface. 4. Provides a full asset conversion pipeline. 5. Portable and Open Source. 3D Models, Asset Import, Game Development https://assimp.org/ https://assimp-docs.readthedocs.io/en/latest/ https://github.com/assimp/assimp/blob/master/Build.md Aces: https://hprc.tamu.edu/software/aces/ Aces: 5.2.5 Open Asset Import Library (short name: Assimp) is a portable Open Source library to import various well-known 3D model formats in a uniform manner. The most recent version also knows how to export 3D files and is therefore called Assimp. The library provides a C++ interface. There are also bindings for various other languages available. Assimp aims to provide a full asset conversion pipeline for use in game engines or real-time rendering systems
astropy Faster Computational Software Library Physical Sciences Astrophysics Astronomy & Planetary Sciences Astropy enhances usability and collaboration among astronomy Python packages. Provides Tools For Astronomical Research In Python, Supports Celestial Coordinate Transformations & Manipulations, Handles Spectral Data & Analysis, Includes Functionality For Time & Date Calculations, Offers Tools For Fits File Handling & Manipulation, Provides Support For Cosmological Calculations Python Library, Astronomy, Astrophysics, Astronomical Research, Data Analysis https://www.astropy.org/ https://docs.astropy.org/en/stable/ https://learn.astropy.org/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.3.1 Astropy is a community-driven Python library for astronomy and astrophysics. It aims to provide core functionality and common tools needed for astronomical research. Astropy includes modules for celestial coordinate systems, spectral manipulations, units and constants, time and dates, FITS file handling, and cosmological calculations.
at-spi2-atk Aces, Faster Interface Library Computer & Information Sciences General General Applications that provide accessibility through the ATK interfaces need a way to translate those interfaces to AT-SPI2 DBus calls. This module, at-spi2-atk, provides that translation bridge.
Description Source: https://gitlab.gnome.org/Archive/at-spi2-atk
Provides an interface for assistive technologies to access and interact with the ATK accessibility library, supports the creation and manipulation of accessible components in graphical user interfaces, enables assistive technologies to receive and respond to events from ATK objects. Assistive Technology, Accessibility, User Interface https://gitlab.gnome.org/Archive/at-spi2-atk https://gitlab.gnome.org/Archive/at-spi2-atk Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.38.0
Faster: 2.34.1, 2.38.0
at-spi2-atk is the Assistive Technology Service Provider Interface (AT-SPI) for the ATK toolkit, which allows assistive technologies to interact with graphical user interfaces.
at-spi2-core Aces, Faster Library Accessibility Software Computer Science General General AT-SPI2-Core is the central component of the Assistive Technology Service Provider Interface, providing APIs for assistive technologies to interact with Linux desktop applications, thereby enhancing accessibility for users with disabilities. 1. Provides accessibility support for people with disabilities.
2. Allows assistive technologies to query and interact with GUI applications.
3. Enables developers to make their applications accessible to assistive technologies.
Accessibility, Assistive Technology, Gui Applications https://gitlab.gnome.org/GNOME/at-spi2-core/ https://gnome.pages.gitlab.gnome.org/at-spi2-core/libatspi/ https://wiki.gnome.org/Accessibility/ATK/BestPractices Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.40.3, 2.44.1, 2.46.0, 2.49.91
Faster: 2.34.0, 2.38.0, 2.40.3, 2.44.1, 2.46.0, 2.49.91
AT-SPI (Assistive Technology Service Provider Interface) is a protocol that allows assistive technologies to interact with and control applications.
atac-seq-pipeline Anvil Application Bioinformatics Sciences Biology The ENCODE ATAC-seq pipeline is used for quality control and statistical signal processing of short-read sequencing data, producing alignments and measures of enrichment.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/atac-seq-pipeline/atac-seq-pipeline.html
https://www.encodeproject.org/atac-seq/ https://github.com/ENCODE-DCC/atac-seq-pipeline Anvil: https://www.rcac.purdue.edu/software/atac-seq-pipeline Anvil: 2.1.3
ataqv Anvil Tool Computational Biology Biological Sciences Genomics, Epigenetics Bioinformatics Ataqv is a toolkit for measuring and comparing ATAC-seq results.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/ataqv/ataqv.html
ataqv provides quality control metrics, differential accessibility analysis, peak calling, and signal enrichment analysis for ATAC-seq and DNase-seq data. Quality Control, Differential Accessibility Analysis, Peak Calling, Signal Enrichment Analysis https://github.com/ParkerLab/ataqv https://parkerlab.github.io/ataqv/ Anvil: https://www.rcac.purdue.edu/software/ataqv Anvil: 1.3.0 ataqv is a software tool designed for comparing ATAC-seq and DNase-seq data to identify signal quality metrics and differential accessibility profiles.
atk Aces, Faster Simulation Software Computational Software Physical Sciences Condensed Matter Physics Physical Sciences ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
Description Source: https://hprc.tamu.edu/software/aces/
ATK enables simulations based on density functional theory (DFT) for electronic structure calculations, molecular dynamics (MD) simulations for atomistic modeling, and a combination of both in quantum mechanics/molecular mechanics (QM/MM) approaches. It supports a wide range of materials properties and advanced analysis tools. Computational Chemistry, Materials Science, Quantum Mechanics, Molecular Dynamics https://gitlab.gnome.org/Archive/atk https://docs.gtk.org/atk/ https://wiki.gnome.org/Accessibility/ATK/BestPractices Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.36.0, 2.38.0
Faster: 2.34.1, 2.36.0, 2.38.0
The Amsterdam Modeling Suite (AMS) offers a comprehensive set of programs for computational chemistry. One of the key components is the Atomistix ToolKit (ATK) for quantum mechanical and classical atomistic simulations of materials.
atlas Darwin Analysis Tool Genomic Data Analysis Biological Sciences Genomics Biological Sciences A library for Numerical Weather Prediction and Climate Modelling 1. Genomic data management
2. Variant calling
3. Visualization tools
4. Interactive interface
5. Large dataset analysis
Genomics, Sequencing, Data Analysis, Visualization https://github.com/ecmwf/atlas https://sites.ecmwf.int/docs/atlas/c++/ https://confluence.ecmwf.int/display/ATLAS/User+guide?preview=/66984475/66984474/Atlas-user-guide-0.8.0.pdf Atlas is a powerful software for managing and visualizing genomic sequencing data. It allows users to analyze large datasets, perform variant calling, and visualize results in an interactive and user-friendly interface.
atop Delta System Monitoring Tool Monitoring Computer & Information Sciences General General Atop is an ASCII full-screen performance monitor for Linux that is capable of reporting the activity of all processes, daily logging of system and process activity for long-term analysis, highlighting overloaded system resources by using colors, etc.
Description Source: https://www.atoptool.nl/
Real-Time System Monitoring, Resource Utilization Tracking, Dynamic & Interactive Display, Process-Level Monitoring, Detailed System Statistics, Ability To Log Data For Future Analysis System Monitor, Performance Analysis, Resource Utilization, Process Activity, System Statistics https://www.atoptool.nl/ https://github.com/Atoptool/atop https://www.atoptool.nl/perftrain.php Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2.5.0 Atop is an advanced interactive system monitor that includes a variety of functionalities for monitoring and analyzing system performance. It provides a real-time overview of system performance, resource utilization, and process activity.
atp Delta Analytical Tool Biological Molecule Biological Sciences Cell Biology Biochemistry & Molecular Biology Abnormal Termination Processing (ATP) is a tool that monitors Cray system user applications. If an application encounters a fatal signal, ATP will handle the signal and perform analysis on the dying application.
Description Source: https://cpe.ext.hpe.com/docs/debugging-tools/atp.1.html
1. Energy carrier in cells
2. Involved in cellular processes like metabolism, muscle contraction, and cell signaling
3. Provides energy for biochemical reactions
Biology, Biochemistry, Cellular Processes https://cpe.ext.hpe.com/docs/debugging-tools/atp.1.html https://hpctools.readthedocs.io/en/latest/debug_atp.html https://cpe.ext.hpe.com/docs/debugging-tools/atp.1.html#example-run Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 3.15.1 ATP (Adenosine triphosphate) is a molecule that carries energy within cells. It is considered the energy currency of life and is involved in various cellular processes.
atram Anvil Genomic Assembly Bioinformatics Biological Sciences Genetics Cell Biology aTRAM (automated target restricted assembly method) is an iterative assembler that performs reference-guided local de novo assemblies using a variety of available methods.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/atram/atram.html
Automated Assembly Of Targeted Genomic Regions, Designed For Capturing & Assembling Large Genomic Regions, Works With Whole-Genome Shotgun Data, Specifically Tailored For Organelle Assemblies Genomics, Bioinformatics, Assembly https://github.com/juliema/aTRAM https://github.com/juliema/aTRAM/blob/master/doc/introduction.md https://github.com/juliema/aTRAM/blob/master/doc/introduction.md Anvil: https://www.rcac.purdue.edu/software/atram Anvil: 2.4.3 atram is a software package that is developed to automate the assembly of targeted genomic regions from whole-genome shotgun data. It is specifically designed for capturing and assembling large genomic regions, such as mitochondria, chloroplasts, and other organelles.
atropos Anvil Trimming Tool Ngs Analysis Biological Sciences Genomics Bioinformatics Atropos is a tool for specific, sensitive, and speedy trimming of NGS reads.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/atropos/atropos.html
1. Adapter detection and trimming
2. Quality filtering and read trimming
3. Support for multiple sequencing platforms
4. Parallel processing for improved efficiency
Ngs, Read Trimming, Adapter Detection https://github.com/jdidion/atropos https://atropos.readthedocs.io/en/1.1/ https://atropos.readthedocs.io/en/1.1/guide.html Anvil: https://www.rcac.purdue.edu/software/atropos Anvil: 1.1.17, 1.1.31 Atropos is a software tool designed for read trimming and adapter detection in Next Generation Sequencing (NGS) data. It aims to accurately identify and remove adapter sequences, poly-A tails, and other types of unwanted sequences from NGS reads.
attrdict3 Aces, Faster Library Python Library Computer & Information Sciences Sciences Computer Science AttrDict is an MIT-licensed library that provides mapping objects that allow their elements to be accessed both as keys and as attributes.
Description Source: https://github.com/pirofti/AttrDict3
Attribute Access To Dictionary Keys, Nested Dictionary Support, Easy To Use & Intuitive Python Library, Dictionary Wrapper https://github.com/pirofti/AttrDict3 https://pypi.org/project/attrdict3/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.0.2
Faster: 2.0.2
attrdict3 is a Python library that provides a dictionary-like object that allows accessing keys like attributes, providing a more convenient way to work with nested dictionaries.
augur Anvil Sequence Analysis Tool Bioinformatics Tool Biological Sciences Phylogenetics Bioinformatics Augur is the bioinformatics toolkit we use to track evolution from sequence and serological data.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/augur/augur.html
Phylogenetic Analysis Of Viral Genomes, Pipeline For Viral Sequence Data Analysis, Phylogenetic Inference, Visualization Of Results Bioinformatics, Phylogenetics, Viral Genomes, Sequence Analysis https://github.com/nextstrain/augur https://docs.nextstrain.org/projects/augur/en/stable/ https://docs.nextstrain.org/projects/augur/en/stable/examples/examples.html Anvil: https://www.rcac.purdue.edu/software/augur Anvil: 14.0.0, 15.0.0 Augur is a bioinformatics tool designed for phylogenetic analysis of viral genomes. It provides a pipeline for analyzing viral sequence data, performing phylogenetic inference, and visualizing the results.
augustus Anvil, Bridges-2 Bioinformatics Tool Gene Prediction Biological Sciences Genomics Bioinformatics AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally.
Description Source: https://bioinf.uni-greifswald.de/augustus/
1. Gene prediction using probabilistic model
2. Prediction of coding regions in eukaryotic genomes
3. Incorporation of RNA-Seq data for improved gene prediction accuracy
Gene Prediction, Eukaryotes, Bioinformatics https://bioinf.uni-greifswald.de/augustus/ https://github.com/Gaius-Augustus/Augustus/tree/master https://vcru.wisc.edu/simonlab/bioinformatics/programs/augustus/docs/tutorial2015/training.html Anvil: https://www.rcac.purdue.edu/software/augustus
Bridges-2: https://www.psc.edu/resources/software/augustus
Anvil: 3.4.0, 3.5.0
Bridges-2: 3.4.0
Augustus is a gene prediction software for eukaryotes that uses a probabilistic model to predict genes on genomic sequences. It is widely used in bioinformatics to identify coding regions in DNA sequences.
autoconf Aces, Darwin, Faster, Kyric Build Tools Software Development Engineering & Technology General General Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
Description Source: https://www.gnu.org/software/autoconf/
1. Generates configure scripts for software packages.
2. Helps in checking system features, setting up variables, and creating makefiles.
3. Enables the creation of software that can be compiled on different Unix-like systems.
4. Facilitates the customization and configuration of software build processes.
5. Aids in reducing the complexity of software builds across multiple platforms.
Build Automation, Software Configuration, Makefiles https://www.gnu.org/software/autoconf/ https://www.gnu.org/software/autoconf/manual/ https://www.lrde.epita.fr/~adl/autotools.html,https://www.sourceware.org/autobook/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.69, 2.71
Faster: 2.69, 2.71
Autoconf is a tool for producing configure scripts for building, installing, and packaging software on Unix-like systems. It assists in the process of automating the configuration of software packages and generating portable makefiles.
autoconf-archive Kyric Service Utilities General General The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script.
Description Source: https://github.com/autoconf-archive/autoconf-archive
https://github.com/autoconf-archive/autoconf-archive https://www.gnu.org/software/autoconf-archive/
autodock Anvil Bioinformatics Tool Molecular Docking Biological Sciences Drug Discovery Biology AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
Description Source: https://autodock.scripps.edu/
Docking Of Small Molecules To Protein Receptors, Prediction Of Binding Modes & Binding Affinities, Analysis Of Molecular Interactions, Virtual Screening For Drug Discovery Computational Chemistry, Molecular Docking, Virtual Screening https://autodock.scripps.edu/ https://autodock.scripps.edu/documentation/documentation/ https://ccsb.scripps.edu/projects/docking/ Anvil: https://www.rcac.purdue.edu/software/autodock Anvil: 2020.06 AutoDock is a suite of automated docking tools designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
autodock-gpu Faster Simulation Software Research Tool Biological Sciences Structural Biology Bioinformatics AutoDock-GPU is an accelerated version of AutoDock4 that is hundreds of times faster than the original single-CPU docking code.
Description Source: https://autodock.scripps.edu/
1. Molecular docking simulations for predicting binding modes.
2. Utilizes GPU acceleration for faster processing.
3. Allows for virtual screening of large compound libraries.
4. Effective tool for studying protein-ligand interactions.
5. Generates detailed reports on docking results.
Molecular Modeling, Molecular Docking, Biomolecular Interactions, Gpu Acceleration https://autodock.scripps.edu/ https://github.com/ccsb-scripps/AutoDock-GPU https://ccsb.scripps.edu/projects/docking/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.5.3-Cuda-11.3.1 AutoDock-GPU is a molecular modeling tool that allows for molecular docking simulations to predict the binding modes of small molecules with biomacromolecules. It utilizes GPU acceleration to significantly speed up the docking process.
autodock-vina Faster Application Docking, Structural Biology Sciences Biology AutoDock Vina is an open-source program for doing molecular docking. AutoDock Vina is one of the docking engines of the AutoDock Suite. https://vina.scripps.edu/ https://vina.scripps.edu/manual/ https://vina.scripps.edu/tutorial/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.1.2-Linux_X86
automake Aces, Faster, Kyric Compiler Build Tools Engineering & Technology General General GNU Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards. Automake requires the use of GNU Autoconf.
Description Source: https://www.gnu.org/software/automake/automake.html
Automates the generation of Makefiles for software projects, simplifies the process of building software, supports the GNU build system, assists in maintaining project consistency and portability. Build Automation, Software Development, Compilers https://www.gnu.org/software/automake/automake.html https://www.gnu.org/software/automake/manual/automake.html https://www.lrde.epita.fr/~adl/autotools.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.16.2, 1.16.3, 1.16.4, 1.16.5
Faster: 1.16.1, 1.16.2, 1.16.3, 1.16.4, 1.16.5
Automake is a build automation tool that automatically generates makefiles for software compilation.
autotools Aces, Faster, Kyric, Stampede3 Build Automation Development Tools Computer & Information Sciences Software Development Software Engineering, Systems, & Development Autotools refers to a suite of tools including Autoconf, Automake, and Libtool used in software development for ensuring portability and simplifying the build process. Autoconf is for creating configure scripts, Automake for generating Makefiles, and Libtool for handling shared libraries. 1. Configuration scripts generation for software builds
2. Dependency tracking and handling
3. Portable Makefiles generation
4. Simplified cross-platform compilation
5. Integration with various programming languages and build systems
Programming, Software Development, Build Automation https://autotools.info https://autotools.info/examples.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 20200321, 20210128, 20210726, 20220317
Faster: 20180311, 20200321, 20210128, 20210726, 20220317
Kyric: Autotools
Stampede-3: 1.4
Autotools is a suite of programming tools designed to assist in making source code packages portable across different Unix-like systems. It includes autoconf, automake, libtool, and others and is commonly used in open-source software projects.
aws-cli Anvil, Delta Command Line Tool Devops & Cloud Tools Computer & Information Sciences, Engineering & Technology General General The AWS Command Line Interface (AWS CLI) is a unified tool to manage your AWS services.
Description Source: https://aws.amazon.com/cli/
1. Unified tool to manage various AWS services from the command line.
2. Provides commands for a wide range of AWS services including EC2, S3, Lambda, etc.
3. Supports scripting and automation of AWS tasks.
4. Easy installation and configuration.
Aws, Command Line Interface, Cloud Management https://aws.amazon.com/cli/ https://docs.aws.amazon.com/cli/ https://aws.amazon.com/training/ Anvil: https://www.rcac.purdue.edu/software/aws-cli
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Anvil: 2.4.15
Delta: 2.13.14
The AWS Command Line Interface (CLI) is a unified tool to manage AWS services from the command line. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts.
awscli Faster Development Tool Command Line Interface Tool Computer & Information Sciences General General The AWS Command Line Interface (AWS CLI) is a unified tool to manage your AWS services.
Description Source: https://aws.amazon.com/cli/
Interact With Various Aws Services, Control Multiple Aws Resources, Automate Aws Tasks, Access & Manage Aws Cli Configuration Cloud Computing, Command Line Interface, Aws Services https://aws.amazon.com/cli/ https://docs.aws.amazon.com/cli/ https://aws.amazon.com/training/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.11.21 The AWS Command Line Interface (CLI) is a unified tool that provides a consistent interface for interacting with various Amazon Web Services (AWS) through the command line. It allows users to manage AWS services and resources directly from the terminal.
axl Faster Framework Scientific Computing Physical Sciences Atomic Simulation Environment Other Natural Sciences AXL is a cross-platform C/C++ support library tailored for large projects, addressing specialized needs like compiler/parser writing and asynchronous IO. 1. Enable seamless collaboration with ASE in Python. 2. Provides tools for exchanging Python objects. 3. Facilitates interaction with various computational materials science software packages in a unified framework. Computational Software, Python Library, Materials Science, Software Collaboration https://github.com/vovkos/axl?tab=readme-ov-file https://github.com/vovkos/axl?tab=readme-ov-file https://vovkos.github.io/axl/build-guide/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 20220413 The Application Exchange Library (Axl) is a software framework that provides a comprehensive suite of tools for collaborating with ASE (Atomic Simulation Environment) in Python. Axl facilitates the exchange of python objects for interacting with different computational materials science software packages.
bactopia Anvil Pipeline Bioinformatics Tool Biological Sciences Genetics Biological Sciences Bactopia is a flexible pipeline for complete analysis of bacterial genomes.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bactopia/bactopia.html
Quality Control Of Sequencing Data, Genome Assembly, Functional Annotation, Comparative Genomics, Identification Of Antibiotic Resistance Genes, Phylogenetic Analysis Bioinformatics, Genomics, Bacterial Genome Analysis, Pipeline https://github.com/bactopia/bactopia https://bactopia.github.io/latest/ https://bactopia.github.io/latest/tutorial/ Anvil: https://www.rcac.purdue.edu/software/bactopia Anvil: 2.0.3, 2.1.1, 2.2.0, 3.0.0 Bactopia is a bioinformatics pipeline that leverages best practices and state-of-the-art tools to perform bacterial genome analysis. It automates the process of quality control, assembly, annotation, and more, providing researchers with a streamlined workflow for analyzing bacterial genomes.
bali-phy Anvil, Faster Bioinformatics Tool Computational Biology Biological Sciences Phylogenetics, Comparative Genomics Bioinformatics Bali-phy is a tool for bayesian co-estimation of phylogenies and multiple alignments via MCMC.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bali-phy/bali-phy.html
Some core features of bali-phy include Bayesian inference of phylogenetic trees, estimation of evolutionary rates and divergence times, handling large-scale datasets efficiently, and conducting rigorous statistical analyses. Bayesian Inference, Phylogenetics, Evolutionary Biology, Genomics https://github.com/bredelings/BAli-Phy https://bali-phy.org/ https://bali-phy.org/Tutorial4.html Anvil: https://www.rcac.purdue.edu/software/bali-phy
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 3.6.0
Faster: 3.6.0, 3.6.1
bali-phy is a software package for Bayesian inference of phylogenies, evolutionary rates, and divergence times. It is particularly designed for large-scale comparative genomic studies.
bam-readcount Anvil Command Line Tool Bioinformatics Tool Biological Sciences Bioinformatics Genomics Bam-readcount is a utility that runs on a BAM or CRAM file and generates low-level information about sequencing data at specific nucleotide positions.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bam-readcount/bam-readcount.html
Summarizes Bam File Reads At Specific Genomic Positions, Useful For Variant Calling & Coverage Assessment, Flexible Output Formats For Downstream Analysis Bioinformatics, Genomics, Variant-Calling, Coverage-Assessment https://github.com/genome/bam-readcount https://github.com/genome/bam-readcount https://github.com/genome/bam-readcount/tree/master/tutorial Anvil: https://www.rcac.purdue.edu/software/bam-readcount Anvil: 1.0.0 bam-readcount is a program that summarizes reference-aligned reads from a BAM file. It is useful for generating read counts at specific genomic positions, such as for variant calling or assessing coverage.
bamgineer Anvil Development Tool Code Generation Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Bamgineer is a tool that can be used to introduce user-defined haplotype-phased allele-specific copy number variations (CNV) into an existing Binary Alignment Mapping (BAM) file with demonstrated applicability to simulate somatic cancer CNVs in phased whole-genome sequencing datsets.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bamgineer/bamgineer.html
1. Genetic programming for code generation and modification. 2. Evolves programs to match specified functionality. 3. Supports C/C++ programming languages. Genetic Programming, Code Generation, C/C++ https://github.com/pughlab/bamgineer https://github.com/pughlab/bamgineer https://github.com/pughlab/bamgineer/blob/master/docs/input_preparation.md Anvil: https://www.rcac.purdue.edu/software/bamgineer Anvil: 1.1 Bamgineer is a software tool designed for generating and modifying C/C++ source code using a genetic programming approach. It utilizes genetic programming to evolve programs to match a given target set of functionality.
bamkit Faster Tool Computational Biology Biological Sciences Sciences Biology Tools for common BAM file manipulations.
Description Source: https://github.com/hall-lab/bamkit
BamKit provides functionalities for parsing BAM files, extracting alignment statistics, filtering reads, marking duplicates, sorting reads, and indexing BAM files. Bioinformatics, Hpc Tools https://github.com/hall-lab/bamkit Faster: https://hprc.tamu.edu/software/faster/ Faster: 2017.04.12 BamKit is a toolkit for analyzing and manipulating BAM files, which are binary sequence alignment/map format files commonly used in bioinformatics for storing mapped sequence data.
bamliquidator Anvil Data Analysis Tool Bioinformatics Tool Biological Sciences Chip-Seq & Atac-Seq Data Analysis Genetics Bamliquidator is a set of tools for analyzing the density of short DNA sequence read alignments in the BAM file format.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bamliquidator/bamliquidator.html
1. Identifying enriched regions (peaks) in ChIP-seq and ATAC-seq data
2. Calculating fold enrichment compared to control data
3. Generating statistics and visualization of peak sets
4. Providing options for customization and integration with downstream analysis tools
Bioinformatics, Hpc Tools https://github.com/BradnerLab/pipeline/wiki/bamliquidator https://github.com/BradnerLab/pipeline/wiki/bamliquidator Anvil: https://www.rcac.purdue.edu/software/bamliquidator Anvil: 1.5.2 bamliquidator is a tool for finding biologically-relevant peak sets in high-throughput sequencing data, particularly ChIP-seq and ATAC-seq data. It helps in identifying enriched regions (peaks) by calculating the fold enrichment compared to control data.
bamsurgeon Anvil Mutation Simulation Bioinformatics Tool Biological Sciences Sciences Biology Bamsurgeon are tools for adding mutations to .bam files, used for testing mutation callers.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bamsurgeon/bamsurgeon.html
1. Spike in synthetic single nucleotide variants (SNVs)
2. Introduce insertions and deletions (indels) at specified genomic locations
3. Add de novo structural variants (SVs) to a given genomic position
4. Allow for customization of mutation rate, allele frequency, and mutation type
5. Test variant calling pipelines by simulating mutations in a controlled manner
Genomic Data, Mutation Simulation, Variant Calling, Bioinformatics https://github.com/adamewing/bamsurgeon https://github.com/adamewing/bamsurgeon/blob/master/doc/Manual.pdf https://github.com/adamewing/bamsurgeon Anvil: https://www.rcac.purdue.edu/software/bamsurgeon Anvil: 1.2 bamsurgeon is a toolkit for adding mutations to a .bam file for use in testing variant calling pipelines. It can be used to spike in synthetic SNVs, indels, and/or denovo SVs to specific genomic coordinates.
bamtools Aces, Anvil, Bridges-2, Expanse, Faster Toolkit Analysis & Manipulation Tools Biological Sciences Sciences Biology BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
Description Source: https://github.com/pezmaster31/bamtools/wiki
Efficient Bam File Reading & Writing, Tools For Filtering, Sorting, Merging, Indexing Bam Files, Support For Extracting Regions, Statistics, & Alignments From Bam Files, Integration With Other Bioinformatics Tools Bioinformatics, Bam Files, Sequence Alignment, Toolkit https://github.com/pezmaster31/bamtools https://github.com/pezmaster31/bamtools/wiki https://genome.sph.umich.edu/wiki/BamUtil:_convert Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/bamtools
Bridges-2: https://www.psc.edu/resources/software/bamtools
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.5.2
Anvil: 2.5.1, 2.5.2
Bridges-2: 2.5.1
Expanse: 2.5.1
Faster: 2.5.2
BamTools is a software toolkit for manipulating BAM (Binary Alignment Map) files. It provides both a C++ API for BAM file input and output, and a command-line tool for performing various operations on BAM files.
bamutil Anvil Utility Data Manipulation Biological Sciences Genomics Bioinformatics Bamutil is a collection of programs for working on SAM/BAM files.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bamutil/bamutil.html
Sorting Bam Files, Merging Bam Files, Indexing Bam Files, Filtering Bam Files Bam Files, Sequence Alignment/Map Format, Bioinformatics, Data Manipulation https://github.com/statgen/bamUtil https://genome.sph.umich.edu/wiki/BamUtil https://genome.sph.umich.edu/wiki/Category:BamUtil Anvil: https://www.rcac.purdue.edu/software/bamutil Anvil: 1.0.15 BamUtil is a versatile utility that provides a range of operations for manipulating BAM files, which are binary versions of the Sequence Alignment/Map (SAM) format used in bioinformatics for storing mapped sequencing data. It offers a variety of functions for sorting, merging, indexing, and filtering BAM files efficiently.
banner Delta Commercial Administrative Software Social Sciences General General The banner program is used to print large letters of a given text. If the text is not given on the command line, it will be read from stdin.
Description Source: https://linuxcommandlibrary.com/man/banner
Banner offers modules for student registration, course management, academic advising, billing and payments, financial aid processing, human resources management, reporting and analytics, and more. It provides integration with various systems to streamline administrative processes. Administrative Software, Higher Education, Student Information System, Academic Records, Financial Aid Management, Human Resources Management https://linuxcommandlibrary.com/man/banner https://www.ibm.com/docs/en/aix/7.3?topic=b-banner-command#banner__title__5 https://www.ibm.com/docs/en/aix/7.3?topic=b-banner-command#banner__title__5 Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 1.3.5 Banner is a comprehensive administrative software solution designed for higher education institutions to manage student information, academic records, financial aid, human resources, and other key administrative functions.
barrnap Anvil Sequence Analysis Tool Bioinformatics Tool Biological Sciences Sequence Analysis Genomics Barrnap: Basic Rapid Ribosomal RNA Predictor. Barrnap predicts the location of ribosomal RNA genes in genomes.
Description Source: https://github.com/tseemann/barrnap
1. Identify ribosomal RNA sequences in DNA data.
2. Utilizes a profile hidden Markov model (HMM) for accurate prediction.
3. Rapid and efficient rRNA prediction.
4. Helps in annotating rRNA genes in genomic data.
Bioinformatics, Genomics, Sequence Analysis, Ribosomal RNA, DNA Sequencing https://github.com/tseemann/barrnap https://github.com/tseemann/barrnap?tab=readme-ov-file#options https://github.com/tseemann/barrnap?tab=readme-ov-file#usage Anvil: https://www.rcac.purdue.edu/software/barrnap Anvil: 0.9.4 Barrnap is a software tool for rapid ribosomal RNA prediction. It identifies rRNA sequences in DNA sequence data using a profile hidden Markov model (HMM) that is more tuned to ribosomal RNA genes.
basenji Anvil Genomics Tool Deep Learning Framework Biological Sciences Regulatory Genomics Genomics Basenji is a tool for sequential regulatory activity predictions with deep convolutional neural networks.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/basenji/basenji.html
Utilizes Convolutional Neural Networks (Cnns) For Regulatory Genomics, Predicts Transcriptional Regulation By Learning Patterns Of Chromatin Accessibility, Histone Modification, & Transcription Factor Binding, Performs Genome Sequence Segmentation & Regulatory Element Prediction Deep Learning, Regulatory Genomics, Transcriptional Regulation https://github.com/calico/basenji https://github.com/calico/basenji https://github.com/calico/basenji?tab=readme-ov-file#tutorials Anvil: https://www.rcac.purdue.edu/software/basenji Anvil: 0.5.1 Basenji is a deep learning framework for regulatory genomics that leverages convolutional neural networks (CNNs) to predict transcriptional regulation by learning the patterns of chromatin accessibility, histone modification, and transcription factor binding.
bat Bridges-2 Analysis Tool Bioinformatics Tool Biological Sciences Bioinformatics Genetics bat tries to achieve the following goals: Provide beautiful, advanced syntax highlighting, integrate with Git to show file modifications, be a drop-in replacement for (POSIX) cat, offer a user-friendly command-line interface.
Description Source: https://github.com/sharkdp/bat?tab=readme-ov-file#project-goals-and-alternatives
- Sequence Alignment, - Phylogenetic Analysis, - Motif Discovery, - Sequence Annotation Bioinformatics, Computational Biology https://github.com/sharkdp/bat https://github.com/sharkdp/bat https://github.com/sharkdp/bat?tab=readme-ov-file#how-to-use Bridges-2: https://www.psc.edu/resources/software/bat Bridges-2: 0.23.0 BAT (Bioinformatics Analysis Tool) is a bioinformatics software suite designed for the analysis of biological sequence data.
bayescan Anvil Analysis Tool Bioinformatics Biological Sciences Population Genetics Genetics BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bayescan/bayescan.html
1. Detection of loci under selection from genetic data
2. Bayesian model comparisons
3. Differentiation between selected and neutral loci using FST values
Genetic Analysis, Natural Selection, Bayesian Model Comparison https://cmpg.unibe.ch/software/BayeScan/ https://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf https://evomics.org/wp-content/uploads/2016/01/BayeScan_BayeScEnv_exercises.pdf Anvil: https://www.rcac.purdue.edu/software/bayescan Anvil: 2.1 BayeScan is a tool used for detecting natural selection from genetic data. It is based on Bayesian model comparisons that enable the identification of loci that are under selection compared to neutral loci. BayeScan uses FST values to differentiate between selected and neutral loci.
bazam Anvil Bioinformatics Tool Data Analysis Biological Sciences Genomics Genetics Bazam is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bazam/bazam.html
Structural Genetic Variant Analysis, Sequencing Data Interpretation, Data Visualization Tools Computational Software, Bioinformatics, Genomics https://github.com/ssadedin/bazam https://github.com/ssadedin/bazam https://github.com/ssadedin/bazam?tab=readme-ov-file#simple-example
https://github.com/ssadedin/bazam?tab=readme-ov-file#advanced-example
Anvil: https://www.rcac.purdue.edu/software/bazam Anvil: 1.0.1 Bazam is a computational software tool developed for analyzing and visualizing structural genetic variants from sequencing data. It provides researchers with a comprehensive set of functionalities to analyze and interpret genomics data.
bazel Aces, Bridges-2, Faster Build & Testing Tools Development Tools & Techniques Engineering & Technology General General Bazel is an open-source build and test tool similar to Make, Maven, and Gradle. It uses a human-readable, high-level build language. Bazel supports projects in multiple languages and builds outputs for multiple platforms. Bazel supports large codebases across multiple repositories, and large numbers of users.
Description Source: https://bazel.build/about/intro
Bazel provides advanced caching and parallel execution for faster builds, support for multiple languages, robust dependency analysis, and scalable resource management. Build Tool, Software Testing, Dependency Management, Resource Management https://bazel.build/ https://bazel.build/docs https://bazel.build/docs#tutorials
https://bazel.build/start/cpp
Aces: https://hprc.tamu.edu/software/aces/
Bridges-2: https://www.psc.edu/resources/software/bazel
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.7.2, 4.2.2, 5.1.1, 6.3.1
Bridges-2: 3.7.1
Faster: 0.26.1, 0.29.1, 2.0.0, 3.6.0, 3.7.2, 4.2.2, 5.1.1, 6.3.1
Bazel is a build tool that helps to build and test software of any size, quickly and reliably.
bbmap Aces, Anvil, Bridges-2, Faster Bioinformatics Tool Sequence Alignment Tool Biological Sciences Sequence Analysis Genomics Bbmap is a short read aligner, as well as various other bioinformatic tools.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bbmap/bbmap.html
1. High-speed short read aligner. 2. Capable of mapping DNA sequences to a reference genome. 3. Includes various bioinformatics tools for sequence analysis and assembly. 4. Supports various file formats. Bioinformatics, DNA Sequencing, Sequence Alignment https://sourceforge.net/projects/bbmap/ https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/ Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/bbmap
Bridges-2: https://www.psc.edu/resources/software/bbmap
Faster: https://hprc.tamu.edu/software/faster/
Aces: 38.90
Anvil: 38.93, 38.96
Bridges-2: 39.01
Faster: 38.90, 38.96
BBMap is a fast and accurate short-read aligner for mapping DNA sequences to a reference genome. It also includes various bioinformatics tools for sequence alignment, mapping, assembly, and analysis.
bbtools Anvil Tool Bioinformatics Biological Sciences Sciences Biology BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bbtools/bbtools.html
Some core features of BBTools include read trimming to remove adapters and low-quality bases, error correction to improve read accuracy, reference mapping for aligning reads to a reference genome, metagenomics analysis for taxonomic classification of sequences, and various utility programs for filtering and manipulating sequencing data. Bioinformatics, Sequencing, High-Throughput, DNA, Metagenomics https://jgi.doe.gov/data-and-tools/software-tools/bbtools/ https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/ Anvil: https://www.rcac.purdue.edu/software/bbtools Anvil: 39.00 BBTools is a suite of bioinformatics tools designed for use with high-throughput DNA sequencing data. It includes various programs for read trimming, error correction, reference mapping, metagenomics analysis, and more.
bcftools Anvil, Bridges-2, Expanse, Faster Bioinformatics Tool Computational Software Biological Sciences Bioinformatics Genomics BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
Description Source: https://samtools.github.io/bcftools/howtos/index.html
Some core features of bcftools include variant calling, filtering and comparison of VCF/BCF files, genotype calling, statistical tests for association studies, subsetting and merging VCF files, and generating consensus sequences. Variant Calling, Genomics, Bioinformatics https://github.com/samtools/bcftools https://samtools.github.io/bcftools/bcftools.html Anvil: https://www.rcac.purdue.edu/software/bcftools
Bridges-2: https://www.psc.edu/resources/software/bcftools
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 1.13, 1.14, 1.17
Bridges-2: 1.10.2
Expanse: 5Zeidhh
Faster: 1.14
bcftools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart (BCF). It provides functionality for filtering, viewing, converting, and annotating variant data.
bcl2fastq Anvil Sequence Data Processing Bioinformatics Biological Sciences Sciences Biology BCL2FASTQ is a software tool that converts raw sequencing data from Illumina sequencing instruments into the FASTQ format, enabling bioinformatic analysis of genomic sequences. Some core features of bcl2fastq include demultiplexing of sequencing data, barcode processing, quality score calculation, adapter trimming, and outputting high-quality FASTQ files ready for further analysis. Sequencing Data, Fastq Files, Illumina Sequencers https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf https://www.youtube.com/watch?v=gz3H_pcLe7c Anvil: https://www.rcac.purdue.edu/software/bcl2fastq Anvil: 2.20.0 bcl2fastq is a software tool developed by Illumina that converts base call files (BCL) generated by Illumina sequencers into FASTQ files, which are commonly used for downstream sequence data analysis.
beagle Anvil Library Computational Biology Biological Sciences Phylogenetics Genetics Beagle is is a software package for phasing genotypes and for imputing ungenotyped markers.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/beagle/beagle.html
Beagle offers support for a wide range of DNA and protein substitution models, parallel processing on multiple CPU cores, and SIMD vectorization to accelerate likelihood calculations. It also includes functionalities for handling large datasets efficiently. Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations https://faculty.washington.edu/browning/beagle/beagle.html https://faculty.washington.edu/browning/beagle/beagle_5.4_18Mar22.pdf https://faculty.washington.edu/browning/beagle/run.beagle.01Mar24.d36.example Anvil: https://www.rcac.purdue.edu/software/beagle Anvil: 5.1_24Aug19.3E8, 5.1 Beagle is a high-performance software library for phylogenetic inference using maximum likelihood methods. It can be used for reconstructing large phylogenetic trees from molecular sequence data with high efficiency and accuracy.
beagle-lib Faster Library Bioinformatics Sciences Biology BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
Description Source: https://github.com/beagle-dev/beagle-lib
1. High-performance likelihood calculations for phylogenetic inference. 2. Implementing the BEAGLE API for efficient computation on both CPU and GPU architectures. 3. Provides functionalities for assessing sequence evolution on large phylogenetic trees. 4. Supports parallel processing for faster calculations. 5. Optimized for handling complex evolutionary models and large datasets efficiently. Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics https://github.com/beagle-dev/beagle-lib https://github.com/beagle-dev/beagle-lib?tab=readme-ov-file#documentation Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.1.2, 4.0.0 Beagle-lib is a high-performance library for evaluating the likelihood of sequence evolution on phylogenetic trees. It is designed to implement the BEAGLE (Broad-platform Evolutionary Analysis General Likelihood Evaluator) application programming interface (API) for helping in tasks related to phylogenetic inference in computational biology.
beast Faster Tool Statistical Analysis Biological Sciences Evolutionary Biology Systems Biology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
Description Source: https://www.beast2.org/
1. Bayesian phylogenetic inference
2. Divergence time estimation
3. Molecular dating
4. Cross-platform compatibility
5. MCMC methods for parameter estimation
Bioinformatics, Computational Biology, Phylogenetics, Molecular Evolution, Bayesian Analysis https://www.beast2.org/ https://www.beast2.org/xml/index.html https://www.beast2.org/tutorials/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.6.7, 2.7.3 BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC (Markov Chain Monte Carlo) methods. It is widely used for phylogenetic inference, divergence time estimation, and molecular dating.
beast1 Expanse Application Bioinformatics Sciences Biology BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
Description Source: https://beast.community/
https://github.com/beast-dev/beast-mcmc https://beast.community/ https://beast.community/getting_started Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: A4Ztrbb, Uuirrt3
beast2 Anvil, Expanse Tool Bioinformatics Biological Sciences Phylogenetics Ecology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
Description Source: https://www.beast2.org/
1. Bayesian inference for molecular sequences analysis
2. Estimation of species trees, gene trees, divergence times, substitution rates, and demographic parameters
3. Wide range of substitution models and clock models
4. Incorporation of fossil constraints and birth-death models
5. Advanced Markov chain Monte Carlo (MCMC) algorithms
6. Integration with other tools like BEAGLE library for high-performance computing
Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference https://www.beast2.org/ https://www.beast2.org/xml/index.html https://www.beast2.org/tutorials/ Anvil: https://www.rcac.purdue.edu/software/beast2
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 2.6.3, 2.6.4, 2.6.6
Expanse: Bhuvd2X, Ymaff6C
BEAST2 is a cross-platform program for Bayesian evolutionary analysis of molecular sequences. It is widely used for estimating species trees, gene trees, divergence times, substitution rates, and demographic parameters using various models of sequence evolution.
beautifulsoup Aces, Faster Library Python Library For Parsing Computer Science General Beautiful Soup is a Python library for pulling data out of HTML and XML files. It works with your favorite parser to provide idiomatic ways of navigating, searching, and modifying the parse tree.
Description Source: https://www.crummy.com/software/BeautifulSoup/bs4/doc/
https://www.crummy.com/software/BeautifulSoup/ https://www.crummy.com/software/BeautifulSoup/bs4/doc/ https://www.datacamp.com/tutorial/web-scraping-using-python
https://www.tutorialspoint.com/beautiful_soup/beautiful_soup_quick_guide.htm
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.10.0, 4.11.1, 4.12.2
Faster: 4.10.0
bedops Anvil, Bridges-2 Command-Line Tool Genomic Data Analysis Tool Biological Sciences Genomics Bioinformatics BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
Description Source: https://bedops.readthedocs.io/en/latest/
Set Operations On Genomic Intervals, Comparisons & Statistical Analyses, Highly Efficient & Flexible Data Analysis Tools, Support For Various Genomic Data Formats, Command-Line Interface Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis https://bedops.readthedocs.io/en/latest/ https://bedops.readthedocs.io/en/latest/content/reference.html https://bedops.readthedocs.io/en/latest/content/usage-examples.html Anvil: https://www.rcac.purdue.edu/software/bedops
Bridges-2: https://www.psc.edu/resources/software/bedops
Anvil: 2.4.39
Bridges-2: 2.4.39
BEDOPS is a suite of tools for flexible and highly efficient genomic data analysis. It provides a wide range of operations for working with genomic data, such as set operations, comparisons, and statistical calculations.
bedtools Aces, Anvil, Bridges-2, Faster Application Bioinformatics Biological Sciences Sciences Biology Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. This is an older version of bedtools2.
Description Source: https://bedtools.readthedocs.io/en/latest/
Bedtools enables users to intersect, merge, count, complement, and shuffle genomic intervals from multiple files. It facilitates the identification of overlaps between different genomic features, such as peaks, gene annotations, and other genomic regions. Bioinformatics, Genomics, Data Analysis, Tool https://github.com/arq5x/bedtools https://bedtools.readthedocs.io/en/latest/ https://bedtools.readthedocs.io/en/latest/content/example-usage.html
https://sandbox.bio/tutorials/bedtools-intro
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/bedtools
Bridges-2: https://www.psc.edu/resources/software/bedtools
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.31.0
Anvil: 2.30.0, 2.31.0
Bridges-2: 2.29.2, 2.30.0
Faster: 2.30.0
Bedtools is a software suite for the comparison, manipulation, and annotation of genomic features in multiple formats.
bedtools2 Expanse Tool Genomic Analysis Biological Sciences Sciences Biology Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
Description Source: https://bedtools.readthedocs.io/en/latest/
1. Intersecting genomic intervals
2. Merging overlapping features
3. Comparing genomic files
4. Filtering and manipulating genomic data
5. Calculating coverage and overlaps
6. Handling multiple file formats
Genomic Data Analysis, Bed Files, Bioinformatics https://github.com/arq5x/bedtools2 https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html https://bedtools.readthedocs.io/en/latest/content/example-usage.html
https://sandbox.bio/tutorials/bedtools-intro
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 5Anbfkq Bedtools2 is a powerful suite of tools for manipulating genomic features and annotations. It allows users to perform a wide range of tasks on genomic intervals, such as intersecting, merging, comparing, and analyzing BED, GFF, VCF, and other common genomic file formats.
berkeley-db Expanse, Kyric Library Developer Support Computer Science Storage, Hpc Applications Berkeley DB is a family of embedded key-value database libraries providing scalable high-performance data management services to applications.
Description Source: https://docs.oracle.com/database/bdb181/
https://www.oracle.com/database/technologies/related/berkeleydb.html https://libdb.org/docs/db/5.3.21/ https://docs.oracle.com/database/bdb181/
https://www.oracle.com/database/technologies/berkeleydb-db-faq.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 18.1.40
berkeley-upc Faster Programming Language Developer Support Computer Science Hpc Applications, Parallel Computing Unified Parallel C (UPC) is an extension of the C programming language designed for high performance computing on large-scale parallel machines.The language provides a uniform programming model for both shared and distributed memory hardware.
Description Source: https://upc.lbl.gov/
https://upc.lbl.gov/ https://upc.lbl.gov/docs/ https://upc.lbl.gov/demos/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 2022.10.0
binutils Aces, Darwin, Faster System Software Development Tools Computer & Information Sciences General General The GNU Binutils are a collection of binary tools. The main ones are: ld (the GNU linker), as (the GNU assembler), and gold (a new, faster, ELF only linker).
Description Source: https://www.gnu.org/software/binutils/
Binutils provides essential tools for creating, modifying, and analyzing executable and object files. It includes utilities for linking object files into executables, assembling source code into object files, creating archives, and more. Binutils supports a wide range of binary formats and architectures. Binary Tools, Linker, Assembler, Object Files https://www.gnu.org/software/binutils/ https://sourceware.org/binutils/docs-2.42/ https://sourceware.org/binutils/docs-2.34/ld/Options.html#Options Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.32, 2.35, 2.36.1, 2.37, 2.38, 2.39, 2.40
Faster: 2.28, 2.30, 2.31.1, 2.32, 2.34, 2.35, 2.36.1, 2.37, 2.38, 2.39, ...
Binutils is a collection of binary tools, including linker (ld), assembler (as), archiver (ar), and other tools to manipulate object files and executables.
bio-db-hts Faster Data Analysis Library Biological Sciences Genomics Bioinformatics Perl interface to HTS library for DNA sequencing.
Description Source: https://metacpan.org/author/AVULLO
Access & Retrieve Hts Data, Manipulate & Analyze Biological Sequence Data, Support For Various Types Of High-Throughput Sequencing Technologies, Integrates With Other Bioinformatics Tools & Libraries Python Library, High Throughput Sequencing, Biological Sequence Data, Bioinformatics https://github.com/Ensembl/Bio-DB-HTS https://metacpan.org/dist/Bio-DB-HTS Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.01 Bio-db-hts is a Python library that provides an easy-to-use interface for working with HTS (High Throughput Sequencing) data. It allows users to access, manipulate, and analyze biological sequence data obtained from high-throughput sequencing technologies.
bioawk Anvil, Faster Scripting Tool Bioinformatics Tool Biological Sciences Computational Biology Bioinformatics Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bioawk/bioawk.html
1. Process and extract information from common bioinformatics file formats such as SAM, BAM, VCF, FASTQ, and GFF.
2. Perform complex data manipulation tasks using custom scripts and commands.
3. Integrate seamlessly with existing bioinformatics pipelines and tools.
4. Handle large-scale datasets efficiently and effectively.
Bioinformatics, Data Processing, File Formats, Data Analysis https://github.com/lh3/bioawk https://github.com/lh3/bioawk https://github.com/lh3/bioawk?tab=readme-ov-file#examples Anvil: https://www.rcac.purdue.edu/software/bioawk
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 1.0
Faster: 1.0
Bioawk is an extension of the AWK programming language, with added functionality specifically designed for processing bioinformatics data. It is an efficient tool for manipulating and analyzing biological data in various formats.
biobambam Anvil Bioinformatics Tools Tools Biological Sciences Genomics Genetics Biobambam is a collection of tools for early stage alignment file processing.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/biobambam/biobambam.html
1. Efficient processing of BAM files
2. Multi-threaded algorithms for improved performance
3. Sorting, merging, indexing, and filtering BAM files
4. Focus on high-throughput sequencing data
5. Compatibility with SAMtools and BAMtools
Bioinformatics, Data Processing, High-Throughput Sequencing https://gitlab.com/german.tischler/biobambam2 https://gitlab.com/german.tischler/biobambam2 Anvil: https://www.rcac.purdue.edu/software/biobambam Anvil: 2.0.183 Biobambam is a set of tools for processing BAM files, with a focus on high-throughput sequencing data. It provides efficient and multi-threaded algorithms for tasks such as sorting, merging, indexing, and filtering BAM files.
biocontainers Anvil, Stampede3 Containerization Bioinformatics Tools Biological Sciences Sciences Biology BioContainers is a community-driven project that provides the infrastructure and basic guidelines to create, manage and distribute bioinformatics packages (e.g conda) and containers (e.g docker, singularity).
Description Source: https://biocontainers-edu.readthedocs.io/en/latest/what_is_biocontainers.html
Containerized Bioinformatics Tools & Workflows, Facilitates Reproducibility In Bioinformatics Analyses, Enables Easy Packaging & Distribution Of Bioinformatics Software, Supports Multiple Container Technologies Like Docker & Singularity Bioinformatics, Containers, Reproducibility, Software Packaging, Workflow Management https://biocontainers.pro/ https://biocontainers-edu.readthedocs.io/en/latest/ https://biocontainers-edu.readthedocs.io/en/latest/examples.html Anvil: https://www.rcac.purdue.edu/software/biocontainers
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Anvil: Default
Stampede-3: 0.1.0
BioContainers is a project that provides bioinformatics tools and workflows in a containerized format, making it easier to package, distribute, and run bioinformatics software in a reproducible manner.
bioconvert Anvil Converter Utility Tool Biological Sciences Sciences Biology Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bioconvert/bioconvert.html
1. Conversion between various bioinformatics file formats.
2. Support for common formats such as FASTA, FASTQ, SAM, BAM, BED, VCF, and more.
3. Command-line interface for batch processing of files.
4. Efficient and reliable conversion process.
5. Customizable options for format conversion.
Bioinformatics, Data Conversion, File Format https://github.com/bioconvert/bioconvert https://bioconvert.readthedocs.io/en/dev/ https://bioconvert.readthedocs.io/en/dev/tutorial.html Anvil: https://www.rcac.purdue.edu/software/bioconvert Anvil: 0.4.3, 0.5.2, 0.6.1, 0.6.2 Bioconvert is a tool for converting between different bioinformatics file formats. It supports a wide range of formats commonly used in bioinformatics analysis and allows for easy and efficient conversion from one format to another.
bioformats Bridges-2 Library Bioinformatics Biological Sciences Sciences Biology Bio-Formats is a software tool for reading and writing image data using standardized, open formats.
Description Source: https://www.openmicroscopy.org/bio-formats/
1. Reading and writing support for various biological image formats.
2. Ability to convert between different image data formats.
3. Efficient handling of large and complex image datasets.
4. Integration with popular programming languages and analysis tools.
Bioinformatics, Imaging, Biological Data, Data Formats https://www.openmicroscopy.org/bio-formats/ https://bio-formats.readthedocs.io/en/v7.3.0/ https://bio-formats.readthedocs.io/en/v7.3.0/about/index.html#help Bridges-2: https://www.psc.edu/resources/software/bioformats Bridges-2: 6.10.1 Bioformats is a software library that provides reading and writing support for a wide range of biological data formats. It aims to simplify the access and integration of diverse image data types in scientific research.
biom-format Faster Data Management Tool Data Format Biological Sciences Genomics Bioinformatics The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. Desciption Source: https://biom-format.org/ Standardized Format For Biological Data, Supports Storage Of Biological Sequence Data, Sample Metadata, & Taxonomic Unit Information, Facilitates Sharing & Integration Of Data From Different High-Throughput Technologies Biological Data, High-Throughput Technologies, Data Sharing https://biom-format.org/ https://biom-format.org/documentation/index.html https://biom-format.org/documentation/quick_usage_examples.html#examples
https://biom-format.org/documentation/table_objects.html#examples
Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.1.12 BIOM (Biological Observation Matrix) format is a unified format to store biological sequence data, sample data, and observed taxonomic units. It provides a standard mechanism to represent, store, and share data generated by different high-throughput technologies such as marker gene surveys.
bioperl Aces, Faster Library Bioinformatics Tool Biological Sciences Bioinformatics Genetics The Bioperl Project is an international association of users & developers of open source Perl tools for bioinformatics, genomics and life science.
Description Source: https://bioperl.org/index.html
Parsing & Manipulation Of Sequence Data (DNA, RNA, Proteins), Sequence Alignment, Sequence Search & Retrieval From Databases, Phylogenetic Analysis Tools, Structure Analysis Tools, Interface With Other Bioinformatics Tools & Databases Bioinformatics, Computational Biology, Sequence Analysis, Perl https://bioperl.org/index.html https://bioperl.org/howtos/index.html https://github.com/bioperl/bioperl-live/tree/master/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.7.8
Faster: 1.7.2, 1.7.8
BioPerl is a collection of Perl modules that provide an easy-to-use and comprehensive toolkit for bioinformatics tasks. It is specifically designed to assist biologists in writing code to analyze biological data and perform various bioinformatics tasks.
biopython Aces, Anvil, Faster Python Library Library Biological Sciences Molecular Biology Bioinformatics Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
Description Source: https://biopython.org/
Sequence & Structure Manipulation, File Parsing (E.G., Fasta, Genbank), Blast, Ncbi Entrez Utilities, Phylogenetics & Population Genetics, Protein Structure Analysis, Sequence Motif Discovery Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics https://biopython.org/ https://biopython.org/wiki/Documentation https://biopython.org/DIST/docs/tutorial/Tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/biopython
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.79, 1.81, 1.82
Anvil: 1.70-Np112Py27, 1.70-Np112Py36, 1.78
Faster: 1.75-Python-3.7.4, 1.78, 1.79
Biopython is a set of freely available tools for biological computation written in Python. It provides functionalities for molecular biology, bioinformatics, structural bioinformatics, and computational biology.
bismark Anvil, Bridges-2, Expanse Alignment & Methylation Analysis Bioinformatics Biological Sciences Epigenetics Genomics Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away.
Description Source: https://www.bioinformatics.babraham.ac.uk/projects/bismark/
1. Alignment of bisulfite treated DNA sequencing reads
2. Identification of methylated cytosines
3. Differential methylation analysis
4. Visualization of methylation patterns
5. Compatibility with various sequencing platforms and data formats
Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics https://www.bioinformatics.babraham.ac.uk/projects/bismark/ https://felixkrueger.github.io/Bismark/ https://felixkrueger.github.io/Bismark/bismark/ Anvil: https://www.rcac.purdue.edu/software/bismark
Bridges-2: https://www.psc.edu/resources/software/bismark
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 0.23.0, 0.24.0
Bridges-2: 0.22.3
Expanse: 4Xdflxj
Bismark is a software tool specifically designed for aligning bisulfite treated DNA sequencing reads and methylation calls. It is widely used in epigenetics research to analyze DNA methylation patterns.
bison Aces, Faster, Ookami Parser Generator Development Tools Computer & Information Sciences General General Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
Description Source: https://www.gnu.org/software/bison/
Bison generates bottom-up parsers. It helps in constructing parsers for programming languages and other complex data description languages. Parser Generator, Programming Language Tool https://www.gnu.org/software/bison/ https://www.gnu.org/software/bison/manual/bison.html https://www.gnu.org/software/bison/manual/html_node/Examples.html
https://aquamentus.com/flex_bison.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 3.3.2, 3.7.1, 3.7.6, 3.8.2
Faster: 3.0.4, 3.0.5, 3.3.2, 3.5.3, 3.7.1, 3.7.6, 3.8.2
Ookami: 3.8.1
Bison is a general-purpose parser generator that converts a grammar description for an LALR context-free grammar into a C program to parse that grammar. It is part of the GNU Project.
blacs Darwin Computational Software Library Physical Sciences Computer Science, Engineering Mathematics The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms.
Description Source: https://www.netlib.org/blacs/
1. Enables the development of parallel linear algebra libraries
2. Optimized for high-performance computing environments
3. Support for various matrix operations and parallel communication
4. Efficiently handles large-scale linear algebra problems
Linear Algebra, High-Performance Computing, Parallel Computing https://www.netlib.org/blacs/ https://www.netlib.org/blacs/ https://www.netlib.org/blacs/BLACS/Examples.html The Basic Linear Algebra Communication Subprograms (BLACS) is a collection of routines for dense linear algebra operations that can be used to construct parallel linear algebra software libraries. BLACS is typically used in high-performance computing environments to efficiently solve large-scale linear algebra problems in parallel.
blasr Anvil Mapping Alignment Biological Sciences Sciences Biology Blasr is a read mapping program that maps reads to positions in a genome by clustering short exact matches between the read and the genome, and scoring clusters using alignment.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blasr/blasr.html
Key features of BLASR include alignment of long reads with high error rates, compatibility with Pacific Biosciences sequencing data, support for various input formats such as HDF5 and FASTQ, and customizable parameters for optimization. Alignment, Sequencing, Genomics https://github.com/PacificBiosciences/blasr https://www.pacb.com/wp-content/uploads/SMRT-Tools-Reference-Guide-v8.0.pdf Anvil: https://www.rcac.purdue.edu/software/blasr Anvil: 5.3.5 BLASR is a software tool designed for aligning SMRT sequencing reads to a reference genome. It is developed by Pacific Biosciences and provides accurate mapping of long and noisy reads.
blast Anvil, Bridges-2, Faster Sequence Analysis Tool Bioinformatics Tool Biological Sciences Bioinformatics Biological Sciences BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blast/blast.html
1. High-speed sequence comparison
2. Database search capability
3. Alignment of query sequences with database sequences
4. Identifying homologous sequences
5. Various search parameters for customization
Bioinformatics, Sequence Alignment, Homology Search https://blast.ncbi.nlm.nih.gov/Blast.cgi https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__AlgoBlast.html https://blast.ncbi.nlm.nih.gov/doc/blast-quick-start-guide/
https://www.youtube.com/playlist?list=PL7dF9e2qSW0azL2xOKAtxDW7QI8UU4XZ6
Anvil: https://www.rcac.purdue.edu/software/blast
Bridges-2: https://www.psc.edu/resources/software/blast
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.11.0, 2.13.0
Bridges-2: 2.9.0, 2.11.0
Faster: 2.11.0-Linux_X86_64
BLAST (Basic Local Alignment Search Tool) is a powerful bioinformatics software tool used to search for homologous sequences in protein and nucleotide databases. It compares a query sequence against a chosen sequence database and identifies local sequence similarities.
blast-plus Anvil, Expanse Tool Bioinformatics, Developer Support Sciences Biology Blast+ allows users to perform BLAST searches on their own server without size, volume and database restrictions. BLAST+ can be used with a command line so it can be integrated directly into your workflow.
Description Source: https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html https://github.com/ncbi/blast_plus_docs https://github.com/ncbi/blast_plus_docs?tab=readme-ov-file#section-2---a-step-by-step-guide-using-the-blast-docker-image Anvil: https://www.rcac.purdue.edu/software/blast-plus
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 2.12.0
Expanse: Jrvhcsy
blast+ Aces, Faster, Ookami Bioinformatics Tool Search & Alignment Tool Biological Sciences Genomics Bioinformatics Blast+ allows users to perform BLAST searches on their own server without size, volume and database restrictions. BLAST+ can be used with a command line so it can be integrated directly into your workflow.
Description Source: https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
Search Nucleotide & Protein Databases For Similarity, Identify Homologous Sequences, Infer Functional & Evolutionary Relationships, Highly Efficient Search Algorithms Bioinformatics, Computational Biology, Genomics, Sequence Analysis https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html https://github.com/ncbi/blast_plus_docs https://github.com/ncbi/blast_plus_docs?tab=readme-ov-file#section-2---a-step-by-step-guide-using-the-blast-docker-image Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.13.0, 2.14.1
Faster: 2.9.0, 2.12.0, 2.13.0
Ookami: Gcc8/2.12.0
BLAST+ (Basic Local Alignment Search Tool) is a suite of tools for performing similarity searches of nucleotide and protein databases. It is widely used for comparing biological sequences to identify homologous sequences and infer functional and evolutionary relationships.
blat Bridges-2, Expanse Tool Bioinformatics Biological Sciences Sciences Biology BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases.
Description Source: https://genome.ucsc.edu/cgi-bin/hgBlat
1. Rapid alignment of DNA sequences
2. Ability to handle large genomes
3. Identifying regions of similarity at the nucleotide level
4. Support for genome mapping and finding gene structures
5. User-friendly interface
Sequence Analysis, DNA Alignment, Genomic Analysis https://kentinformatics.com/ https://kentinformatics.com/documentation https://genome.ucsc.edu/training/index.html Bridges-2: https://www.psc.edu/resources/software/blat
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Bridges-2: 36
Expanse: 35
BLAT (BLAST-Like Alignment Tool) is a sequence analysis software used for comparing genomic DNA sequences to the human genome. It is particularly useful for finding regions of similarity between DNA sequences at the nucleotide level.
blender Aces, Faster Visual Arts Software 3D Modeling & Animation Engineering & Technology General General Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
Description Source: https://www.blender.org/about/
3D Modeling, Animation, Simulation, Rendering, Game Creation, Video Editing, Compositing 3D Modeling, Computer Graphics, Animation, Simulation, Open-Source https://www.blender.org/ https://docs.blender.org/manual/en/latest/ https://www.youtube.com/watch?v=TPrnSACiTJ4&list=PLjEaoINr3zgHs8uzT3yqe4iHGfkCmMJ0P
https://en.wikibooks.org/wiki/Blender_3D:_Noob_to_Pro
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.5.0-Linux-X86_64-Cuda-11.7.0
Faster: 3.0.0-Linux-X64, 3.1.2-Linux-X64
Blender is a free and open-source 3D creation suite that supports the entire 3D pipeline – modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
blis Aces, Anvil, Darwin, Faster, Ookami Computational Software Library Computer & Information Sciences Engineering Mathematics BLIS is an award-winning portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
Description Source: https://github.com/flame/blis
High-performance BLAS library, portable and flexible, optimized for various modern architectures, includes a BLISlab for automated performance analysis and tuning. Blas, Linear Algebra, High Performance Computing, Optimization https://github.com/flame/blis https://github.com/flame/blis/blob/master/docs/BLISTypedAPI.md https://github.com/flame/blis/blob/master/docs/Testsuite.md
https://github.com/flame/blis/tree/master/examples/oapi
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/blis
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 0.8.1, 0.9.0
Anvil: 0.8.1
Faster: 0.8.0, 0.8.1, 0.9.0, 2.2-Amd, 3.1-Amd
Ookami: Gcc12.1.0/0.9.0
BLAS (Basic Linear Algebra Subprograms) implemented in native C and suitable for high-performance implementations. BLIS is capable of achieving high levels of performance on various architectures.
blobtools Anvil Bioinformatics Tool Visualization & Analysis Biological Sciences Sciences Biology Blobtools is a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/blobtools/blobtools.html
Some of the core features of BlobTools include taxon assignment, assessment of genome completeness, visualization of assembly statistics, and exploration of metagenomic datasets. Genome Assembly, Data Visualization, Metagenomics https://github.com/DRL/blobtools https://blobtools.readme.io/docs/what-is-blobtools https://blobtools.readme.io/docs/my-first-blobplot Anvil: https://www.rcac.purdue.edu/software/blobtools Anvil: 1.1.1 BlobTools is a software suite for visualizing and analyzing genome assembly data. It allows users to assess the quality and taxonomic composition of a genome assembly using data generated from short-read sequencing technologies.
blosc2 Aces, Faster Compression Library Computer & Information Sciences General General Blosc, an extremely fast, multi-threaded, meta-compressor library.
Description Source: https://www.blosc.org/pages/
1. Multi-dimensional data support
2. High-performance compression and decompression
3. Production-ready meta-compressor library
4. Data storage and retrieval optimization
5. Supported by various programming languages
6. Parallel compression with thread and process-based approaches
High-Performance Computing, Compression, Data Storage, Optimization https://github.com/Blosc/c-blosc2 https://www.blosc.org/c-blosc2/c-blosc2.html https://github.com/Blosc/c-blosc2/tree/main/examples
https://www.youtube.com/watch?v=ER12R7FXosk
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.4.3
Faster: 2.4.3
Blosc2 is a high-performance, production-ready meta-compressor library that provides a simple way to accelerate data storage and retrieval. It focuses on optimizing the handling of large, multi-dimensional data, catering to both compression and decompression operations efficiently.
bmge Anvil Sequence Alignment Tool Bioinformatics Tool Biological Sciences Sequence Analysis Bioinformatics Bmge is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bmge/bmge.html
Alignment Of Homologous DNA Or Protein Sequences, Utilizes Block Mapping & Entropy-Based Techniques, Identification & Removal Of Poorly Aligned Regions, Improves Accuracy Of Multiple Sequence Alignments Bioinformatics, Computational Biology, Sequence Alignment, Sequence Analysis https://bio.tools/bmge https://gensoft.pasteur.fr/docs/BMGE/1.12/ Anvil: https://www.rcac.purdue.edu/software/bmge Anvil: 1.12 BMGE (Block Mapping and Gathering with Entropy) is a software tool designed for the alignment of homologous DNA or protein sequences. It employs block mapping and entropy-based techniques to identify and remove poorly aligned regions, thereby improving the accuracy of multiple sequence alignments.
bohrium Faster High-Performance Computing Tool Array Programming Language Computer & Information Sciences Programming Languages & Compilers Computer Science Bohrium provides automatic acceleration of array operations in Python/NumPy, C, and C++ targeting multi-core CPUs and GP-GPUs. Forget handcrafting CUDA/OpenCL to utilize your GPU and forget threading, mutexes and locks to utilize your multi-core CPU, just use Bohrium!
Description Source: https://bohrium.readthedocs.io/index.html
1. Python integration with APL-like array operations. 2. Just-in-time (JIT) compilation for high performance. 3. Automatic parallelization for CPU and GPU execution. 4. Seamless integration with existing Python libraries and tools. High-Performance Computing, Array Programming, Python Integration, Gpu Acceleration https://github.com/bh107/bohrium https://bohrium.readthedocs.io/index.html https://bohrium.readthedocs.io/users/cpp.html#code-snippets Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.11.0.Post60 Bohrium is a high-performance JIT-compiled array programming language that extends Python with support for versatile array operations using a subset of the APL syntax. It automatically parallelizes and runs programs on the CPU and GPU.
bokeh Aces, Faster Library Visualization Computer & Information Sciences General General Bokeh is a Python library for creating interactive visualizations for modern web browsers. It helps you build beautiful graphics, ranging from simple plots to complex dashboards with streaming datasets.
Description Source: https://docs.bokeh.org/en/latest/
Some core features of Bokeh include creating versatile plots, dashboards, and data applications in Python; interactive visualizations with a large selection of visual elements such as plots, tables, and sliders; seamless integration with Jupyter notebooks; support for streaming and real-time data; and the ability to create interactive, web-ready plots which can be easily shared. Visualization, Interactive Plots, Data Visualization https://bokeh.org/ https://docs.bokeh.org/en/latest/ https://realpython.com/python-data-visualization-bokeh/
https://programminghistorian.org/en/lessons/visualizing-with-bokeh
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.4.1, 2.4.2, 2.4.3
Faster: 1.4.0-Python-3.7.4, 2.0.2-Python-3.8.2, 2.2.3, 2.4.2, 2.4.3
Bokeh is an interactive visualization library for modern web browsers. It provides elegant, concise construction of versatile graphics with high-performance interactivity over large or streaming datasets in a browser window.
boost Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Kyric, Ookami, Stampede3 Development Tool Library Computer & Information Sciences Engineering Computer Science, Software Engineering, Systems, & Development BLAST (Basic Local Alignment Search Tool) is a bioinformatics software program used for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. It's widely used for identifying similarities, understanding evolutionary relationships, and finding functional and structural homologues among sequences in large databases, making it a crucial tool in genomic and proteomic research. Extensive C++ Libraries, Support For Various Tasks & Data Structures, Enhanced Functionality For C++ Programming C++ Libraries, Programming Support, Efficiency Enhancement https://www.boost.org/ https://www.boost.org/doc/libs/1_84_0/ https://www.boost.org/doc/libs/1_77_0/more/getting_started/index.html
https://theboostcpplibraries.com/
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/boost
Bridges-2: https://www.psc.edu/resources/software/boost
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 1.76.0, 1.77.0, 1.79.0, 1.81.0, 1.82.0, 1.83.0
Anvil: 1.74.0
Bridges-2: 1.75-Gcc10.2.0, 1.75.0-Intel20.4
Delta: 1.83.0
Expanse: Bbnd4Wn, Ckwq57R, ...
Faster: 1.71.0, 1.72.0, 1.74.0, 1.76.0, 1.77.0, 1.79.0, 1.81.0, 1.82.0
Kyric: 1.73.0
Ookami: Gcc8.5/1.83
Stampede-3: 1.85.0
Boost is a set of C++ libraries that provides support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. It aims to extend the functionality of C++ programming language and make it more efficient and powerful.
boost.mpi Aces Middleware Library Computer & Information Sciences Software Engineering, Systems, & Development Other Computer & Information Sciences Boost.MPI is a library for message passing in high-performance parallel applications.
Description Source: https://www.boost.org/doc/libs/1_84_0/doc/html/mpi/tutorial.html
Boost.MPI provides an intuitive C++ interface for MPI operations, allowing for seamless integration of parallelism into C++ applications. It offers support for point-to-point and collective communication, synchronizations, and parallel computational operations. Mpi, Parallel Computing, C++ https://github.com/boostorg/mpi https://www.boost.org/doc/libs/1_84_0/doc/html/mpi.html https://www.boost.org/doc/libs/1_84_0/doc/html/mpi/tutorial.html Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.79.0 Boost.MPI is a peer-reviewed, free, open-source, portable, and fully-standard library implementation of the Message Passing Interface (MPI) for C++.
boost.python Aces, Faster Library Scientific Library Computer & Information Sciences Engineering Mathematics Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
Description Source: https://www.boost.org/doc/libs/1_84_0/libs/python/doc/html/index.html
Bi-Directional Communication Between C++ & Python, Automatic Mapping Of Basic C++ Types To Python, Support For Exposing C++ Classes, Functions, & Modules To Python, Ability To Call Python Code From C++ & Vice Versa, Extensive Documentation & Community Support C++, Python, Integration, Library https://github.com/boostorg/python https://www.boost.org/doc/libs/1_84_0/libs/python/doc/html/index.html https://boostorg.github.io/python/doc/html/tutorial/index.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.79.0, 1.81.0, 1.83.0
Faster: 1.71.0, 1.76.0, 1.77.0, 1.81.0
Boost.Python is a library used for interfacing Python and C++. It enables seamless integration of C++ code with Python and provides tools to expose C++ classes, functions, and objects to Python scripts, and vice versa.
botorch Faster Bayesian Optimization Library Computational Library Computer & Information Sciences Machine Learning Artificial Intelligence & Intelligent Systems BoTorch (pronounced "bow-torch" / ˈbō-tȯrch) is a library for Bayesian Optimization research built on top of PyTorch, and is part of the PyTorch ecosystem.
Description Source: https://botorch.org/docs/introduction
Modular & Scalable Approach To Bayesian Optimization, State-Of-The-Art Methods For Acquisition Functions, Models, & Optimizers, Implemented In Pytorch For Seamless Integration With Deep Learning Workflows Bayesian Optimization, Pytorch, Machine Learning https://botorch.org/ https://botorch.org/docs/introduction https://botorch.org/tutorials/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.6.0-Python-3.8.6 BoTorch is a library for Bayesian optimization built on PyTorch. It provides a modular and scalable approach to Bayesian optimization, including state-of-the-art methods for acquisition functions, models, and optimizers, all implemented in PyTorch.
bottleneck Faster Data Processing Library Computer & Information Sciences Sciences, Engineering Computer Science, Mathematics Bottleneck is a collection of fast NumPy array functions written in C.
Description Source: https://github.com/pydata/bottleneck
1. Fast NumPy array functions
2. Optimized for performance
3. Ideal for large data sets
4. Written in C for efficiency
Numpy, Array Functions, Performance Optimization https://github.com/pydata/bottleneck https://bottleneck.readthedocs.io/en/latest/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.3.2-Python-3.8.6, 1.3.2-Python-3.9.6 bottleneck is a collection of fast NumPy array functions written in C. It is designed to work in situations where speed is important, particularly for large data sets.
bowtie Anvil, Faster Alignment Tool Bioinformatics Biological Sciences Biological Sciences Genetics Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.
Description Source: https://bowtie-bio.sourceforge.net/manual.shtml
Some core features of Bowtie include ultrafast alignment, memory efficiency, support for gapped alignment, support for multi-core processing, and compatibility with various sequencing platforms. Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment https://bowtie-bio.sourceforge.net/index.shtml https://bowtie-bio.sourceforge.net/manual.shtml https://bowtie-bio.sourceforge.net/tutorial.shtml Anvil: https://www.rcac.purdue.edu/software/bowtie
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 1.3.1
Faster: 1.3.1
Bowtie is a fast and memory-efficient short read aligner for short DNA sequences. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million reads per hour on a typical workstation with a large amount of memory.
bowtie2 Anvil, Bridges-2, Expanse, Faster Sequence Alignment Alignment Tool Biological Sciences Genomics Bioinformatics Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning to relatively long (e.g. mammalian) genomes.
Description Source: https://github.com/BenLangmead/bowtie3
Ultrafast Alignment Of Sequencing Reads To Long Reference Sequences, Memory-Efficient Indexing & Alignment Process, Support For Gapped, Local, & End-To-End Alignment Modes, Alignment & Mapping Of DNA Sequencing Reads, High Accuracy In Finding Alignments, Scalability For Large Genomes & Datasets Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics https://bowtie-bio.sourceforge.net/bowtie2/index.shtml https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml https://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#getting-started-with-bowtie-2-lambda-phage-example Anvil: https://www.rcac.purdue.edu/software/bowtie2
Bridges-2: https://www.psc.edu/resources/software/bowtie2
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.4.2, 2.5.1
Bridges-2: 2.4.2, 2.4.4
Expanse: Ahg6M6S
Faster: 2.4.4, 2.4.5, 2.5.1
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly well-suited for aligning sequencing reads of DNA sequences, such as those generated by high-throughput sequencing technologies.
bracken Anvil Tool Bioinformatics Biological Sciences Metagenomics Microbial Ecology Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bracken/bracken.html
Estimates Species Abundance From Metagenomic Data, Utilizes A Bayesian Framework, Useful For Analyzing Microbial Communities & Microbiome Data Metagenomics, Microbiome, Species Abundance Estimation, Bayesian Analysis https://github.com/jenniferlu717/Bracken https://ccb.jhu.edu/software/bracken/index.shtml?t=manual https://github.com/jenniferlu717/Bracken?tab=readme-ov-file#example-abundance-estimation Anvil: https://www.rcac.purdue.edu/software/bracken Anvil: 2.6.1, 2.7 Bracken is a tool that utilizes a Bayesian framework to estimate species abundance from metagenomic data generated by sequencing. It is particularly useful in the analysis of microbial communities and microbiome data.
braker2 Anvil Genome Annotation Tool Computational Software Biological Sciences Bioinformatics Biological Sciences BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/braker2/braker2.html
1. Unsupervised training process for gene prediction based on RNA-Seq data. 2. Integration of RNA-Seq data to improve gene prediction accuracy. 3. Support for both eukaryotic and prokaryotic genomes. 4. High computational efficiency compared to traditional genome annotation tools. Genome Annotation, RNA-Seq Data, Gene Prediction https://github.com/Gaius-Augustus/BRAKER https://bioinf.uni-greifswald.de/augustus/binaries/tutorial2018/BRAKER_userguide.pdf https://www.youtube.com/watch?v=UXTkJ4mUkyg Anvil: https://www.rcac.purdue.edu/software/braker2 Anvil: 2.1.6 BRAKER2 is a novel tool for unsupervised RNA-Seq-based genome annotation. It combines gene prediction and RNA-Seq alignment in an innovative and computational efficient way to improve genome annotations.
brass Anvil Circuit Design & Simulation Simulation Software Engineering & Technology Sciences Biology Brass is used to analyze one or more related BAM files of paired-end sequencing to determine potential rearrangement breakpoints.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/brass/brass.html
Circuit Design, Simulation, Electronic Components Library, User-Friendly Interface Circuit Design, Electronic Simulation, Electronics https://github.com/cancerit/BRASS https://github.com/cancerit/BRASS Anvil: https://www.rcac.purdue.edu/software/brass Anvil: 6.3.4 Brass is a circuit design and simulation software that allows users to create, edit, and simulate electronic circuits. It provides a user-friendly interface for designing and testing circuits for various applications.
breseq Anvil Genome Analysis Tool Bioinformatics Tool Biological Sciences Microbial Genetics Genetics Breseq is a computational pipeline for the analysis of short-read re-sequencing data.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/breseq/breseq.html
1. Identification of mutations in bacterial genomes
2. Detection of single nucleotide variants, insertions, deletions, inversions, and complex polymorphisms
3. Visualization of identified mutations
4. Analysis of microbial evolution within a population
Computational Biology, Bioinformatics, Genomics https://github.com/barricklab/breseq https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/ https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/tutorial_clones.html
https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/tutorial_populations.html
https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/tutorial_barcoded_targeted.html
Anvil: https://www.rcac.purdue.edu/software/breseq Anvil: 0.36.1 Breseq is a computational tool for identifying mutations in bacteria that have evolved in a microbial population. It can detect single nucleotide variants, insertions, deletions, inversions, and complex polymorphisms in bacterial genomes.
brotli Aces, Faster Tool Developer Support General General Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods.
Description Source: https://brotli.org/
1. High compression ratio: Brotli provides better compression ratios compared to the existing compression algorithms. 2. Fast decompression speed: Brotli decompression is highly efficient, making it suitable for use in various applications. 3. Support for multiple platforms: Brotli is available for various platforms including desktop and mobile environments. 4. Open-source: Brotli is an open-source project, allowing for community contributions and improvements. 5. Integration with web browsers: Brotli is supported by major web browsers, enabling faster loading times for web pages. Compression Algorithm, Lossless Compression, Data Compression https://brotli.org/ https://github.com/google/brotli https://kinsta.com/blog/brotli-compression/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.9
Faster: 1.0.9
Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding, and 2nd order context modelling. It is developed by Google and designed to replace the zlib compression.
brotli-python Aces Compression Library Library Computer & Information Sciences Data Compression Computer Science Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods.
Description Source: https://brotli.org/
1. Compression and decompression of data using the Brotli algorithm.
2. Integration with Python applications for efficient data compression.
3. Support for various compression levels and settings.
4. High compression ratio and fast decompression speed.
Compression, Data Compression, Brotli, Python Library https://github.com/python-hyper/brotlicffi https://python-hyper.org/projects/brotlipy/en/latest/ https://github.com/python-hyper/brotlicffi/tree/main/example Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.0.9 brotli-python is a Python binding for the Brotli compression library. It allows users to compress and decompress data using the Brotli algorithm within Python applications.
brunsli Aces, Faster Image Compressor Compression Software Computer & Information Sciences General General Brunsli is a lossless JPEG repacking library. Brunsli allows for a 22% decrease in file size while allowing the original JPEG to be recovered byte-by-byte.
Description Source: https://github.com/google/brunsli
1. Lossless image compression
2. High-speed encoding
3. Efficient compression ratios
4. Fast decoding speeds
Image Compression, Lossless Compression, High-Speed Encoding https://brunsli.dev/ https://github.com/google/brunsli https://github.com/google/brunsli?tab=readme-ov-file#build-instructions Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.1
Faster: 0.1
Brunsli is an advanced lossless image compressor that focuses on high-speed encoding. It aims to achieve significant compression ratios while maintaining fast encoding and decoding speeds.
build Faster Task Automation Development Tools Engineering & Technology General General A simple, correct Python build frontend.
Description Source: https://github.com/pypa/build
Task Automation, Buildfile Configuration, Dependency Management, Plugin System, Integration With Version Control Systems Task Automation, Build Tool, Software Development https://github.com/pypa/build https://build.pypa.io/en/stable/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.10.0 Build is a task automation tool that allows users to define tasks in a buildfile. It is commonly used for compiling source code, running tests, creating distributions, and other repetitive tasks in software development projects.
busco Anvil, Bridges-2 Tools Computational Biology Biological Sciences Genomics Bioinformatics Benchmarking Universal Single-Copy Orthologs (BUSCO) is used for assessing genome assembly and annotation completeness.
Description Source: https://gitlab.com/ezlab/busco
1. Evaluation of genome assembly and gene or protein set completeness. 2. Benchmarking against evolutionarily-informed expectations. 3. Analysis of orthologous genes or proteins. 4. Scalable and versatile for different organisms. Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs https://busco.ezlab.org/ https://busco.ezlab.org/busco_userguide.html https://busco.ezlab.org/busco_userguide.html#running-busco Anvil: https://www.rcac.purdue.edu/software/busco
Bridges-2: https://www.psc.edu/resources/software/busco
Anvil: 5.2.2, 5.3.0, 5.4.1, 5.4.3, 5.4.4, 5.4.5, 5.4.7
Bridges-2: 5.0.0
BUSCO (Benchmarking Universal Single-Copy Orthologs) is a software package that assesses genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content.
bustools Anvil Bioinformatics Tool Data Analysis Tool Biological Sciences Genomics Bioinformatics Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bustools/bustools.html
Mapping Reads To A Reference Genome, Quantifying Unique Molecular Identifiers (Umis), Filtering Input Data Based On Quality Metrics, Error Correcting Umis For Greater Accuracy, Clustering Cells & Analyzing Expression Profiles Single-Cell RNA-Seq, Data Analysis, Bioinformatics, Computational Biology https://bustools.github.io/ https://bustools.github.io/manual https://www.kallistobus.tools/applications/ Anvil: https://www.rcac.purdue.edu/software/bustools Anvil: 0.41.0 bustools is a software package for manipulating single-cell RNA-seq data and performing various analysis tasks such as mapping, quantification, error correction, and filtering. It is specifically designed for analyzing droplet-based single-cell RNA-seq data generated from technologies like 10X Genomics' Chromium platform.
bwa Aces, Anvil, Bridges-2, Expanse, Faster Bioinformatics Tool Alignment Tool Biological Sciences Sciences Biology BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Description Source: https://bio-bwa.sourceforge.net/
Mapping Low-Divergent Sequences, Alignment Of Illumina Sequence Reads, Support For Short & Long Reads, Efficient Memory Usage Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs) https://bio-bwa.sourceforge.net/ https://bio-bwa.sourceforge.net/bwa.shtml https://bioinformatics-core-shared-training.github.io/cruk-bioinf-sschool/Day1/Sequence%20Alignment_July2015_ShamithSamarajiwa.pdf Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/bwa
Bridges-2: https://www.psc.edu/resources/software/bwa
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.7.17
Anvil: 0.7.17
Bridges-2: 0.7.3A
Expanse: 0.7.17
Faster: 0.7.17
Burrows-Wheeler Aligner (BWA) is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW, and BWA-MEM. The BWA-backtrack algorithm is designed for Illumina sequence reads up to 100bp, while BWA-SW and BWA-MEM are for longer Illumina reads, including 100bp reads produced by the HiSeq 2000 platform.
bwameth Anvil Bioinformatics Tool Sequence Alignment Tool Biological Sciences Epigenetics Genetics Bwameth is a tool for fast and accurante alignment of BS-Seq reads.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/bwameth/bwameth.html
The core features of bwameth include alignment of BS-Seq reads, detection of 5-methylcytosine bases, calculation of DNA methylation levels, and visualization of methylation patterns. DNA Methylation, Bisulfite Sequencing, Alignment, Bioinformatics https://github.com/brentp/bwa-meth https://github.com/brentp/bwa-meth https://github.com/brentp/bwa-meth/tree/master/example/ Anvil: https://www.rcac.purdue.edu/software/bwameth Anvil: 0.2.5 Bwameth is a software tool designed for aligning bisulfite-treated sequencing reads (BS-Seq) from targeted bisulfite sequencing experiments with DNA methylation analysis.
byacc Expanse Development Tool Compiler Computer & Information Sciences General General Berkeley Yacc is an LALR(1) parser generator. Berkeley Yacc has been made as compatible as possible with AT&T Yacc. Berkeley Yacc can accept any input specification that conforms to the AT&T Yacc documentation.
Description Source: https://github.com/grandseiken/byacc
byacc generates parsers for context-free grammars, assists in building syntax analysis for programming languages, facilitates the creation of efficient parsers for various applications. Parser Generator, Lalr, Context-Free Grammar https://invisible-island.net/byacc/ https://invisible-island.net/byacc/manpage/yacc.html Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Master byacc is a public domain LALR parser generator which is often used as a replacement for yacc. LALR parsers are used in the generation of efficient parsers for modern programming languages.
bzip2 Aces, Expanse, Faster, Kyric Compression Tool Utility Computer & Information Sciences General General bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
Description Source: https://sourceware.org/bzip2/
1. High compression ratio
2. Fast compression and decompression speeds
3. Open-source and free to use
4. Cross-platform compatibility
5. Efficient use of system resources
File Compression, Data Compression, Utility Software https://sourceware.org/bzip2/ https://sourceware.org/bzip2/manual/manual.html https://www.tutorialspoint.com/unix_commands/bzip2.htm Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.8
Expanse: 1.0.8
Faster: 1.0.6, 1.0.8
bzip2 is a free and open-source file compression program that uses the Burrows-Wheeler algorithm for compression and Huffman coding for decompression. It is designed to be fast and efficient in compressing large files while retaining a high compression ratio.
c-ares Aces, Faster Networking Library Computer & Information Sciences General General c-ares is a C library for asynchronous DNS requests (including name resolves).
Description Source: https://c-ares.org/
Asynchronous Dns Requests, Support For Ipv4 & Ipv6, Thread-Safe Design, Support For Multiple Dns Server Configurations, Compatible With Various Operating Systems Dns, Asynchronous, Networking, Library, C https://c-ares.org/ https://c-ares.org/docs.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.18.1
Faster: 1.17.2, 1.18.1
c-ares is a C library that performs DNS requests and name resolutions asynchronously. It is designed to be lightweight and efficient, providing asynchronous DNS capabilities to applications.
cactus Anvil Simulation Software Scientific Computing Physical Sciences Numerical Relativity Gravitational Physics Cactus is a reference-free whole-genome alignment program, as well as a pagenome graph construction toolkit. Description Source = https://github.com/ComparativeGenomicsToolkit/cactus?tab=readme-ov-file 1. Solves partial differential equations
2. Supports adaptive grid techniques
3. Designed for numerical relativity simulations
4. Utilizes advanced high-performance computing environments
Computational Software, Hpc Tools https://github.com/ComparativeGenomicsToolkit/cactus?tab=readme-ov-file https://www.cactuscode.org/documentation/ReferenceManual.pdf https://www.cactuscode.org/documentation/tutorials/index.html
https://www.cactuscode.org/documentation/UsersGuide.pdf
Anvil: https://www.rcac.purdue.edu/software/cactus Anvil: 2.0.5, 2.2.1, 2.2.3-Gpu, 2.2.3, 2.4.0-Gpu, 2.4.0, 2.5.2-Gpu, 2.5.2, 2.6.5-Gpu, ... Cactus is an open-source software package designed for numerical relativity simulations within the Einstein field equations of general relativity. It provides a framework for solving partial differential equations on adaptive grids in high-performance computing environments.
cafe Anvil Bioinformatics Tool Statistical Analysis Biological Sciences Evolutionary Genomics Genomics Cafe is a computational tool for the study of gene family evolution.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/cafe/cafe.html
Cafe allows users to estimate the birth (duplication) and death (deletion) rates of gene families, assess the significance of gene family size changes, and infer ancestral gene family sizes. It also provides visualizations of the results. Computational Biology, Bioinformatics https://github.com/hahnlab/CAFE5 https://hahnlab.github.io/CAFE/manual.html https://github.com/hahnlab/CAFE5/blob/master/docs/tutorial/tutorial.md Anvil: https://www.rcac.purdue.edu/software/cafe Anvil: 4.2.1, 5.0.0 Cafe is a computational tool for analyzing gene family evolution. It implements a stochastic model to infer the birth-and-death process of gene family evolution.
cairo Aces, Faster Library Graphics Library Computer & Information Sciences Computer Science Graphics Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output.
Description Source: https://cairographics.org/
Cairo supports various output targets including image buffers, PNG files, PDF files, SVG files, PostScript files, and direct rendering to X Window System and Windows surfaces. It offers a simple API for drawing paths, text, and images with advanced features like gradients, patterns, and transformations. Graphics Library, 2D Graphics, Rendering Engine https://cairographics.org/ https://www.cairographics.org/manual/ https://www.cairographics.org/tutorial/
https://zetcode.com/gfx/cairo/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.16.0, 1.17.4, 1.17.8
Faster: 1.16.0, 1.17.4, 1.17.8
Cairo is a 2D graphics library with support for multiple output devices. It provides a vector-based rendering engine for high-quality graphics with full support for transparency and anti-aliasing.
canu Anvil, Faster Bioinformatics Tool Genome Assembler Biological Sciences Genome Assembly, Long-Read Sequencing Genomics, Bioinformatics Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Description Source: https://github.com/marbl/canu
Some of the key features of Canu include error correction, trimming, assembling, and visualization of long-read sequencing data. It also includes support for multi-genome assembly and variant calling. Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics https://github.com/marbl/canu https://canu.readthedocs.io/en/latest/ https://canu.readthedocs.io/en/latest/quick-start.html
https://canu.readthedocs.io/en/latest/tutorial.html
Anvil: https://www.rcac.purdue.edu/software/canu
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.1.1, 2.2
Faster: 2.2
Canu is a software tool that is used for assembling genomes using nanopore sequencing data. It is designed to be efficient and scalable, making it suitable for large and complex genomes.
capstone Aces, Faster Tool Disassembly Framework Computer & Information Sciences Cybersecurity Computer Science Capstone is a lightweight multi-platform, multi-architecture disassembly framework.
Description Source: https://www.capstone-engine.org/
Capstone supports multiple hardware architectures and provides a rich set of APIs for disassembling machine code, including instruction semantics, details, and operand access. It is designed to be lightweight and efficient, making it suitable for various applications such as static code analysis, dynamic binary instrumentation, malware analysis, and more. Disassembly, Binary Analysis, Reverse Engineering https://www.capstone-engine.org/ https://www.capstone-engine.org/documentation.html https://www.capstone-engine.org/documentation.html#programming Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.0.1
Faster: 5.0.1
Capstone is a disassembly framework with the target of becoming the ultimate disasm engine for binary analysis and reversing in the security community. Created by Nguyen Anh Quynh, it is open-source software distributed under the Simplified BSD License.
captum Aces Model Interpretation Interpretability Library Computer & Information Sciences Computer Science Artificial Intelligence, Machine Learning Captum (“comprehension” in Latin) is an open source, extensible library for model interpretability built on PyTorch. Captum helps ML researchers more easily implement interpretability algorithms that can interact with PyTorch models. It also allows researchers to quickly benchmark their work against other existing algorithms available in the library.
Description Source: https://captum.ai/docs/introduction.html
1. Support for various interpretability algorithms such as Integrated Gradients, Feature Ablation, Occlusion, DeepLift, etc. 2. Compatibility with PyTorch for seamless integration into PyTorch-based deep learning workflows. 3. Extensibility to create custom interpretation algorithms or extend existing ones. 4. Visualization tools to aid in the interpretation of model decisions. 5. Facilitates understanding of model behavior and decisions for better model debugging and trustworthiness. Interpretability, Model Interpretation, Deep Learning, Pytorch https://captum.ai/ https://captum.ai/docs/introduction https://captum.ai/tutorials/ Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.5.0 Captum is an extensible library for model interpretation in PyTorch. It provides a flexible and unified API for different interpretability methods and allows users to easily interpret deep learning models.
cartopy Aces, Faster Python Library Visualization Tool Physical Sciences Geophysics & Geochemistry Earth & Environmental Sciences Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.
Description Source: https://github.com/SciTools/cartopy
Supports Various Map Projections & Coordinate Reference Systems, Integration With Matplotlib For Plotting Spatial Data, Ability To Plot Data On Maps, Add Coastlines, Borders, & Gridlines, Provides Tools For Geospatial Data Manipulation & Analysis Geospatial Data Processing, Data Visualization, Python Library, Mapping, Scientific Visualization https://github.com/SciTools/cartopy https://scitools.org.uk/cartopy/docs/latest/ https://github.com/SciTools/cartopy/tree/main/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.20.3, 0.22.0
Faster: 0.20.0, 0.20.3, 0.22.0
Cartopy is a Python package designed for geospatial data processing to produce high-quality visualizations of maps using matplotlib. It aims to simplify and enhance the mapping capabilities in Python, providing rich, interactive, and customized maps for various scientific disciplines.
catch2 Aces, Faster Testing Framework Developer Tools Engineering & Technology Software Engineering, Systems, & Development Computer Science Catch2 is mainly a unit testing framework for C++, but it also provides basic micro-benchmarking features, and simple BDD macros.
Description Source: https://github.com/catchorg/Catch2/tree/devel?tab=readme-ov-file
1. Lightweight and easy to get started with
2. Support for TDD, BDD, and specification by example
3. Extensive set of matchers to write expressive and flexible test specifications
4. Ability to define test cases with minimal boilerplate code
5. Rich command-line interface for executing tests and generating reports
Testing Framework, C++, Unit Testing https://github.com/catchorg/Catch2 https://github.com/catchorg/Catch2/blob/devel/docs/Readme.md https://github.com/catchorg/Catch2/blob/devel/docs/tutorial.md#top Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.4.0
Faster: 2.13.9, 3.4.0
Catch2 is a C++ testing framework that is easy to use, yet powerful. It supports test-driven development, behavior-driven development, and specification by example.
ccache Aces, Faster Compiler Utility Development Tools Engineering & Technology General General Ccache is a compiler cache. It speeds up recompilation by caching previous compilations and detecting when the same compilation is being done again.
Description Source: https://ccache.dev/
Caching Compiled Object Files For Faster Compilation Times, Transparently Intercepting Compiler Calls, Support For Various Compilers & Build Systems, Customizable Cache Size & Behavior, Tracking Dependencies To Invalidate Outdated Cache Entries Compiler Cache, C/C++ Compilation, Build Optimization https://ccache.dev/ https://linux.die.net/man/1/ccache https://ccache.dev/manual/latest.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.6.1, 4.6.3
Faster: 4.6.1
ccache is a compiler cache tool designed to speed up C and C++ compilation by caching previous compilations. It acts as a caching proxy for compilers, storing compiled object files in a cache directory, which can be reused when the same compilation is done again. This reduces compilation times significantly, especially during iterative development processes.
ccdb Delta Curated Data Resource Database Biological Sciences Cell Cycle Regulation Cell Biology CCDB: Cray's comparative debugger features a graphical user interface and extends the comparative debugging capabilities of lgdb, allowing users to easily compare data structures between two executing applications.
Description Source: https://support.hpe.com/hpesc/public/docDisplay?docId=a00113984en_us&page=Cray_Debugger_Support_Tools.html
Access To Curated Cell Cycle-Related Data, Tools For Analyzing Cell Cycle Regulation, Links To Relevant Literature & Resources Cell Cycle, Cell Biology, Database https://cpe.ext.hpe.com/docs/debugging-tools/cpedocs_ccdb/cpedocs_index_chunk.html https://cpe.ext.hpe.com/docs/debugging-tools/cpedocs_ccdb/guide/index.html https://support.hpe.com/hpesc/public/docDisplay?docId=a00113984en_us&page=Using_CCDB.html&docLocale=en_US Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html CCDB (Cell Cycle Database) is a freely accessible, comprehensive resource for the cell cycle community. It provides information and tools to study cell cycle regulation and its role in cancer and other diseases.
cce Delta Compiler/Interpreter Development Tools Computer & Information Sciences Software Engineering Computer Science 1. Lexical analysis and parsing tools
2. Abstract Syntax Tree (AST) generation
3. Code generation and optimization capabilities
4. Integrated development environment for language design and compiler construction
5. Support for various programming languages and target architectures
Compiler, Interpreter, Programming Language, Compiler Construction Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 16.0.1 Compiler Construction Engine (CCE) is a software tool used for building compilers and interpreters. It provides a set of tools and libraries to assist in the creation of programming language implementations.
cce-mixed Delta Electronic Structure Calculation Computational Software Physical Sciences Electronic Structure Of Solids Condensed Matter Physics 1. GW approximation calculations for electronic structure analysis
2. Self-energy calculations
3. Bethe-Salpeter equation solutions for optical excitations
4. Solid-state materials electronic structure analysis
Computational Chemistry, Quantum Mechanics, Electronic Structure Calculations Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 16.0.1 cce-mixed is a software package designed for performing calculations in the framework of many-body perturbation theory for the electronic structure of solids. It focuses on the GW approximation, self-energy calculations, and the solution of the Bethe-Salpeter equation for optical excitations.
ccl Kyric 1. Easy definition of command line arguments with strong typing. 2. Automatic generation of help messages. 3. Support for positional arguments, switches, and flags. 4. No external dependencies. Command Line Interface, C++ Library https://ccl.clozure.com/ https://ccl.clozure.com/docs/ccl.html https://ccl.clozure.com/docs/ccl.html#using-clozure-cl Kyric: Latest, 2021.1.1 CCL (Cpp Command Line Library) is a C++ library targeting Unix platform that makes it easy to define and parse command line arguments. It provides a simple and intuitive way to define and parse command-line arguments for C++ programs.
ccs Anvil Bioinformatics Tool Computational Software Biological Sciences Pbccs is a tool to generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads). Sequence Assembly, Genome Scaffolding, Variant Calling, Haplotype Phasing Bioinformatics, Computational Biology, Sequence Analysis, Genomics Anvil: https://www.rcac.purdue.edu/software/ccs Anvil: 6.4.0 The Consensus Computational Suite (CCS) is a collection of open-source tools and algorithms for analyzing, visualizing, and interpreting data in the context of consensus algorithms. It includes various modules for sequence assembly, genome scaffolding, variant calling, and haplotype phasing.
cd-hit Aces, Anvil, Faster Bioinformatics Software Clustering Tool Biological Sciences Sequence Analysis Bioinformatics Cd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences. 1. Clustering of protein or nucleotide sequences
2. Reducing redundancy in large sequence datasets
3. Generating non-redundant representative sequences
4. Alignment-based and word-counting algorithms
5. Various clustering and similarity threshold options
Sequence Analysis, Clustering, Bioinformatics Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cd-hit
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.8.1
Anvil: 4.8.1
Faster: 4.8.1
cd-hit is a widely used program for clustering and comparing protein or nucleotide sequences. It clusters a large set of sequences to reduce redundancy and generate a non-redundant representative set. This tool is beneficial for sequence analysis, especially in bioinformatics studies.
cdat Faster Tool Data Analysis & Visualization Earth & Environmental Sciences Climate & Global Dynamics Atmospheric Sciences Accessing Climate & Weather Data, Analyzing Large Datasets, Visualizing Data, Performing Complex Data Tasks Climate Data, Weather Data, Data Analysis, Data Visualization Faster: https://hprc.tamu.edu/software/faster/ Faster: 8.2.1-Python-3.8.2 The Climate Data Analysis Tools (CDAT) is an open-source software package that provides capabilities for accessing, analyzing, and visualizing climate and weather data. CDAT is designed to help researchers in the atmospheric and climate sciences analyze large datasets and perform complex data tasks.
cdbtools Anvil Command-Line Utility Database Management Cdbtools is a collection of tools used for creating indices for quick retrieval of any particular sequences from large multi-FASTA files. Key features of cdbtools include the ability to efficiently store and retrieve key-value pairs, support for fast lookups and searches within CDB files, and tools for managing and maintaining CDB databases. Cdb, Command-Line, Data Manipulation Anvil: https://www.rcac.purdue.edu/software/cdbtools Anvil: 0.99 cdbtools is a set of command-line utilities for manipulating and working with Constant Database (CDB) files. These utilities provide functionality for creating, reading, updating, and deleting records in CDB files.
cdo Aces, Anvil, Delta, Faster, Stampede3 Command Line Tool Data Processing & Analysis Earth & Environmental Sciences CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. Supported data formats are GRIB 1/2, netCDF 3/4, SERVICE, EXTRA and IEG. There are more than 600 operators available.
Description Source: https://code.mpimet.mpg.de/projects/cdo
Supports A Wide Range Of File Formats Including Grib, Netcdf, Hdf, & More, Provides Tools For Data Selection, Slicing, Aggregation, Interpolation, Calculation, & Visualization, Enables Batch Processing & Scripting For Automatic Data Processing, Includes Comprehensive Documentation & Support For A Variety Of Operations On Climate Data Climate Data, Data Manipulation, Command Line, Data Analysis https://code.mpimet.mpg.de/projects/cdo https://code.mpimet.mpg.de/projects/cdo/wiki/Cdo#Documentation https://code.mpimet.mpg.de/projects/cdo/wiki/Tutorial Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cdo
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2.0.5
Anvil: 1.9.9
Delta: 2.4.0
Faster: 1.9.10
Stampede-3: 2.3.0
Climate Data Operators (CDO) is a collection of command-line operators for manipulating and analyzing climate and numerical weather prediction (NWP) model data.
cdsapi Aces Api Library Earth & Environmental Sciences Climate/Weather The Climate Data Store (CDS) Application Program Interface (API) is a service providing programmatic access to CDS data.
Description Source: https://cds.climate.copernicus.eu/api-how-to
1. Access climate and weather data from ECMWF's CDS API. 2. Retrieve datasets for various parameters like temperature, precipitation, wind speed, etc. 3. Download data in multiple formats such as NetCDF and GRIB. 4. Simplified authentication process for accessing ECMWF data. 5. Efficient querying and downloading of meteorological data. Python Library, Climate Data, Weather Data https://github.com/ecmwf/cdsapi https://confluence.ecmwf.int/display/CKB/Climate+Data+Store+%28CDS%29+API+Keywords https://cds.climate.copernicus.eu/api-how-to Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.5.1 cdsapi is a Python client library for Climate Data Store (CDS) API, which allows users to access climate and weather data provided by the European Centre for Medium-Range Weather Forecasts (ECMWF).
cegma Anvil Tool Bioinformatics Biological Sciences Genome Assembly Genomics CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome. Prediction Of Core Eukaryotic Genes, Assessment Of Genome Assembly Completeness, Identification Of Conserved Genes In Eukaryotic Genomes Genome Assembly, Core Eukaryotic Genes, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/cegma Anvil: 2.5 CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for predicting core eukaryotic genes in genome assemblies. It is designed to identify a set of conserved genes that are expected to be present in all eukaryotic genomes. CEGMA is commonly used for evaluating the completeness and quality of genome assemblies.
cellbender Anvil Python Library Data Processing Biological Sciences Single-Cell RNA-Seq Data Analysis Genetics Cellbender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. Denoising Single-Cell RNA-Seq Data, Removing Ambient RNA Contamination, Correcting Batch Effects, Addressing Technical Artifacts In Scrna-Seq Datasets Single-Cell RNA-Seq, Data Processing, Denoising, Batch Effects, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/cellbender Anvil: 0.2.0, 0.2.2 CellBender is a Python package for processing, denoising, and removing technical variation from single-cell RNA-seq data. It offers methods for the removal of ambient RNA contamination, batch effects, and other technical artifacts commonly found in single-cell RNA-seq datasets.
cellchat Anvil Python Library Bioinformatics Tool Biological Sciences Single-Cell Analysis Cell Biology CellChat: Inference and analysis of cell-cell communication.
Description Source: https://purduercac-applications.readthedocs.io/en/latest/Biocontainers/r-cellchat/r-cellchat.html
Identification & Visualization Of Ligand-Receptor Interactions, Inference Of Signaling Networks Between Cell Types, Integration Of Scrna-Seq Data To Study Intercellular Communication, Visualization Of Communication Networks & Pathways Single-Cell RNA Sequencing, Cell-Cell Communication, Bioinformatics, Python Package https://github.com/sqjin/CellChat Anvil: https://www.rcac.purdue.edu/software/cellchat CellChat is a Python package designed for cell-cell communication analysis in single-cell RNA-seq data. It provides a comprehensive toolkit for studying ligand-receptor interactions and signaling networks between different cell types within complex tissues.
cellphonedb Anvil Computational Software Bioinformatics Biological Sciences CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions. 1. Curated database of receptors, ligands, and interactions in immune and stromal cells. 2. Provides information on cell-cell communication in biological systems. 3. Enables the analysis of ligand-receptor interactions and signaling networks. 4. Facilitates the study of cell communication in the context of complex tissues and organs. Bioinformatics, Hpc Tools Anvil: https://www.rcac.purdue.edu/software/cellphonedb Anvil: 2.1.7 CellPhoneDB is a publicly available repository of curated receptors, ligands, and interactions between immune and stromal cells.
cellranger Anvil Bioinformatics Biological Sciences Sciences Biology A set of analysis pipelines that perform sample demultiplexing, barcode processing, single cell 3' and 5' gene counting, V(D)J transcript sequence assembly and annotation, and Feature Barcode analysis from single cell data.
Description Source: https://www.10xgenomics.com/support/software/cell-ranger/latest
Demultiplexing, mapping, filtering, counting single-cell RNA-Seq data. Bioinformatics, Single-Cell RNA-Seq, Data Analysis https://www.10xgenomics.com/support/software/cell-ranger/latest https://www.10xgenomics.com/support/software/cell-ranger/latest/resources/cr-command-line-arguments https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials Anvil: https://www.rcac.purdue.edu/software/cellranger Anvil: 6.0.1, 6.1.1, 6.1.2, 7.0.0, 7.0.1, 7.1.0 Cell Ranger is a set of analysis pipelines that process Chromium Single Cell 3’ RNA-seq data. It includes software for demultiplexing, mapping, filtering, and counting single-cell RNA-Seq data.
cellranger-arc Anvil Bioinformatics Tool Data Analysis Tool Biological Sciences Genetics Bioinformatics Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression (GEX), chromatin accessibility, and their linkage. Identification Of Accessible Chromatin Regions (Peaks), Clustering Of Cells Based On Peak Accessibility, Differential Accessibility Analysis Across Clusters Single-Cell Analysis, Chromatin Accessibility, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/cellranger-arc Anvil: 2.0.2 Cell Ranger ARC is a software package for analyzing single-cell chromatin accessibility data. It identifies accessible chromatin regions (peaks), cluster cells based on similarity of peak accessibility, and performs differential accessibility analysis across clusters.
cellranger-atac Anvil Application Bioinformatics Sciences Biology Cell Ranger ATAC is a software application for analyzing and visualizing Single Cell ATAC data produced by the 10x Genomics Chromium platform. Software Description=https://support.10xgenomics.com/single-cell-atac/software/overview/welcome https://support.10xgenomics.com/single-cell-atac/software/overview/welcome https://www.10xgenomics.com/support/single-cell-atac/documentation https://pages.10xgenomics.com/sup-how-to-single-cell-atac-v2.html Anvil: https://www.rcac.purdue.edu/software/cellranger-atac Anvil: 2.0.0, 2.1.0
cellranger-dna Anvil Tool Bioinformatics Biological Sciences Genomics Genetics Analysis Of Single-Cell DNA Sequencing Data, Identification Of Structural Variants, Detection Of Copy Number Variations, Estimation Of Clonality In Individual Cells, Support For Linked-Read Sequencing Technologies Single-Cell DNA Sequencing, Structural Variants, Copy Number Variations, Clonality Analysis, Linked-Read Sequencing Anvil: https://www.rcac.purdue.edu/software/cellranger-dna Anvil: 1.1.0 Cell Ranger DNA is a software package from 10x Genomics that enables the analysis of single-cell DNA sequencing data. It is specifically designed to process single-cell data from linked-read sequencing technologies, such as the 10x Genomics Chromium platform, to identify structural variants, copy number variations, and clonality in individual cells.
cellrank Anvil Python Library Library Biological Sciences Computational Biology Bioinformatics Cellrank is a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. Cell Fate Decision Modeling, Identification Of Cell Transitions, Driver Analysis Of Transitions, RNA Velocity Analysis, Transition Matrices, Attractor Inference Single-Cell RNA Sequencing, Cell Fate Decisions, Cell Transitions, Transcriptional Dynamics, Python Library Anvil: https://www.rcac.purdue.edu/software/cellrank Anvil: 1.5.1 CellRank is a Python library for identifying cell transitions and their drivers in single-cell RNA sequencing data. It provides a comprehensive framework for modeling cell fate decisions using RNA velocity, transition matrices, and attractor inference.
cellrank-krylov Anvil Python Library Computational Software Biological Sciences Cellrank-krylov is the cellrank package with extra libraries that are useful for large datasets. Cell Fate Prediction, Lineage Analysis, Single-Cell RNA Sequencing Data Analysis, Cell Differentiation Trajectories, Identification Of Key Cell States Single-Cell Analysis, Lineage Analysis, RNA Sequencing, Cell Fate Prediction Anvil: https://www.rcac.purdue.edu/software/cellrank-krylov Anvil: 1.5.1 cellrank-Krylov is a Python library designed to provide cell fate prediction and lineage analysis for single-cell RNA sequencing data using Krylov subspace methods. It offers tools for exploring cell differentiation trajectories and uncovering crucial cell states in the data.
cellsnp-lite Anvil Variant Calling Tool Bioinformatics Tool Biological Sciences Single-Cell Genomics Cell Biology cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data, which can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo, which assigns cells to donors and detects doublets, even without genotyping reference. 1. Genotyping of single cells
2. Haplotype inference for diploid cells
3. Detection of single-nucleotide variations (SNVs) and small indels
4. Single-cell RNA sequencing data analysis
5. High accuracy in variant calling
Variant Calling, Single-Cell RNA Sequencing, Genotyping, Haplotype Inference Anvil: https://www.rcac.purdue.edu/software/cellsnp-lite Anvil: 1.2.2 Cellsnp-lite is a variant calling tool for single-cell RNA sequencing data, specifically designed for genotyping and haplotype inference for diploid cells. It allows for accurately detecting single-nucleotide variations, small insertions and deletions, and single-cell genotyping from scRNA-seq data.
celltypist Anvil Bioinformatics Tool Analysis Tool Biological Sciences Single-Cell Omics Bioinformatics Celltypist is a tool for semi-automatic cell type annotation. Marker Gene Detection, Cell Type Identification, Cluster-Based Classification, Unbiased Classification Single-Cell RNA Sequencing, Cell Type Classification, Computational Framework Anvil: https://www.rcac.purdue.edu/software/celltypist Anvil: 0.2.0, 1.1.0 CellTypist is a computational framework for unbiased cell type classification of single-cell RNA sequencing data. It integrates marker gene detection, cell type identification, and cluster-based classification to provide accurate and interpretable cell type annotations.
centrifuge Anvil Analysis Tool Bioinformatics Tool Biological Sciences Metagenomics Microbiology Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. Classification Of Metagenomic Sequencing Data, Utilizes Burrows-Wheeler Transform (Bwt) & Fm-Index, Rapid & Memory-Efficient, Uses A Comprehensive Protein Sequence Database Bioinformatics, Metagenomics, Sequencing Data Analysis, Microbiome Analysis, Computational Biology Anvil: https://www.rcac.purdue.edu/software/centrifuge Anvil: 1.0.4_Beta Centrifuge is a tool used for rapid and sensitive classification of metagenomic sequencing data. It utilizes a Burrows-Wheeler transform (BWT) and FM-index for rapid and memory-efficient classification of reads against a comprehensive and up-to-date protein sequence database.
cereal Expanse Data Serialization Library Computer & Information Sciences cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. Cereal provides functionalities for serializing and deserializing data structures in C++. It supports a wide range of data types, including custom classes, and offers flexibility in serialization formats. Serialization, C++, Library Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 1.3.0 Cereal is a C++11 library for serialization. It is designed to be fast, compact, and have an easy-to-use API.
cesm Faster Computational Software Modeling & Simulation Earth & Environmental Sciences Climate & Global Dynamics Earth & Environmental Sciences The Community Earth System Model is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states.
Description Source: https://www.cesm.ucar.edu/
Fully-Coupled Climate Model, Global Climate Simulations, Multi-Component Model, Advanced Earth System Modeling Capabilities Climate Modeling, Earth System Modeling, Global Climate Simulations https://www.cesm.ucar.edu/models/cesm2 https://escomp.github.io/CESM/versions/cesm2.2/html/introduction.html https://www.youtube.com/playlist?list=PLsqhY3nFckOEX41g8ZUnhGT2c--5kUZ1V Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.1.3 The Community Earth System Model (CESM) is a fully-coupled, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states.
cesm-deps Aces, Faster Libraries & Dependencies Tools & Utilities Earth & Environmental Sciences Sciences The Community Earth System Model is a fully coupled global climate model developed in collaboration with colleagues in the research community. CESM provides state of the art computer simulations of Earth's past, present, and future climate states.
Description Source: https://www.cesm.ucar.edu/
Provides Essential Dependencies & Tools For Cesm Software, Includes Libraries, Compilers, & Other Software Required For Cesm Simulations, Ensures Smooth Operation & Performance Optimization Of Cesm Models Dependencies, Cesm, Earth System Model, Simulation, Software Package https://www.cesm.ucar.edu/models/cesm2 https://escomp.github.io/CESM/versions/cesm2.2/html/introduction.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2
Faster: 2
CESM-DEPS is a set of dependencies and tools for supporting the Community Earth System Model (CESM) software. It includes various libraries, compilers, and software packages necessary for running CESM simulations.
cffi Aces, Faster Interfacing Library Computer & Information Sciences C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation. Easily Call C Functions From Python, Efficiently Share Data Between C & Python, No Need To Write C Code With The Use Of Cffi Apis Foreign Function Interface, C Library Integration, Python Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.15.1
Faster: 1.15.1
CFFI is a Foreign Function Interface between Python and C. It allows calling C code from Python and using Python code from C. It provides a way to interact with foreign functions and call them from Python without having to write any C code.
cfitsio Aces, Faster Data Processing Library Physical Sciences Astronomy Astronomy & Planetary Sciences CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CFITSIO provides simple high-level routines for reading and writing FITS files that insulate the programmer from the internal complexities of the FITS format.
Description Source: https://heasarc.gsfc.nasa.gov/fitsio/
CFITSIO provides a comprehensive set of interfaces for reading, writing, and manipulating FITS files. It supports various data types, compression methods, and image formats commonly used in astronomical and scientific data. Astronomy, Data Processing, File Format, Fits https://heasarc.gsfc.nasa.gov/fitsio/ https://heasarc.gsfc.nasa.gov/fitsio/c/c_user/cfitsio.html https://heasarc.gsfc.nasa.gov/docs/software/fitsio/quick/node2.html
https://fits.gsfc.nasa.gov/fits_libraries.html#c_cfitsio
https://heasarc.gsfc.nasa.gov/docs/software/fitsio/cexamples.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.2.0, 4.3.0
Faster: 3.49, 4.2.0, 4.3.0
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
cfsan-snp-pipeline Anvil Pipeline Bioinformatics Tool Biological Sciences The CFSAN SNP Pipeline is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety. 1. Identification of single nucleotide polymorphisms (SNPs) in bacterial genomes.
2. Processing of raw sequence data from next-generation sequencing (NGS) platforms.
3. Phylogenetic analysis and comparison of bacterial strains based on SNP variations.
4. Visualization tools for SNP analysis results.
5. Integration with other bioinformatics tools and databases for additional analysis.
Bioinformatics, Computational Biology, Sequence Analysis Anvil: https://www.rcac.purdue.edu/software/cfsan-snp-pipeline Anvil: 2.2.1 The cfsan-snp-pipeline is a bioinformatics tool developed by the Center for Food Safety and Applied Nutrition (CFSAN) that is used for identifying single nucleotide polymorphisms (SNPs) from raw sequence data of bacterial genomes.
cgal Aces, Expanse, Faster Algorithm Library Library Computer & Information Sciences Computational Geometry Computer Science CGAL is an open source software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics.
Description Source: https://www.cgal.org/
1. Robust and efficient algorithms for computational geometry
2. Support for a wide range of geometric data structures
3. Implementation of various geometric algorithms, such as convex hulls, triangulations, Voronoi diagrams, and more
4. Integration with other libraries and software tools
5. Extensive documentation and user support
6. Portable and compatible with multiple platforms
Computational Geometry, Geometric Algorithms, Software Library https://www.cgal.org/ https://doc.cgal.org/latest/Manual/dev_manual.html https://doc.cgal.org/latest/Manual/tutorials.html Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.14.3, 5.6
Expanse: Axpdrof, Jrg6Ven, Lnidf3A
Faster: 4.14.3-Python-3.8.2, 4.14.3, 5.2
CGAL (Computational Geometry Algorithms Library) is a software library that provides a wide range of efficient and reliable geometric algorithms for use in various applications in computational geometry, such as mesh generation, geometric processing, visualization, and more. It is designed to be versatile, easy to use, and highly efficient.
cgns Aces File Format Data Exchange Physical Sciences Fluid Dynamics Fluid & Plasma Physics 1. Supports the hierarchical structure of CFD computations.
2. Allows data to be written to a file so that it is portable across different machines and operating systems.
3. Provides mechanisms for modifying data as technologies advance, ensuring long-term viability of CFD data.
4. Offers a range of tools and conventions to support data interoperability.
Computational Software Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.4.0 The CFD General Notation System (CGNS) provides a standard for recording and recovering computer data associated with the numerical solution of the equations of fluid dynamics. It is designed to facilitate the exchange of data between sites and applications, as well as to help stabilize the archiving of fluid dynamics data.
chameleon Aces Library Data Visualization Library Other Computer & Information Sciences Chameleon is a framework written in C which provides routines to solve dense general systems of linear equations, symmetric positive definite systems of linear equations and linear least squares problems, using LU, Cholesky, QR and LQ factorizations. 1. Generate custom color palettes
2. Easily customize color schemes
3. Compatibility with popular data visualization libraries
4. Seamless integration with Python data analysis workflows
Python Library, Data Visualization, Color Palette, Visualization, Python Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.2.0 Chameleon is a Python library for creating customizable color palettes for data visualization purposes. It provides a user-friendly interface to easily generate aesthetically pleasing color schemes for various types of visualizations.
chapel Faster, Ookami Compiler Programming Language Computer & Information Sciences Chapel is a programming language designed for productive parallel computing at scale.
Description Source: https://chapel-lang.org/
Supports A Multithreaded Execution Model With A Partitioned Global Address Space, Provides A High-Level & Expressive Syntax, Offers Support For Data Parallelism, Task Parallelism, & Nested Parallelism, Includes Features For Interoperability With Existing Languages Such As C, C++, & Fortran, Designed For Use In Large-Scale Parallel Computing Environments Parallel Programming, Hpc, High-Performance Computing, Programming Language https://chapel-lang.org/ https://chapel-lang.org/docs/ https://chapel-lang.org/tutorials.html Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Faster: 1.29.0-Mpi
Ookami: 1.33.0
Chapel is an emerging parallel programming language developed by Cray Inc. specifically designed for productive high-performance computing (HPC). It is designed to improve the productivity of parallel programming and provide scalability and portability across various HPC platforms.
charliecloud Aces, Faster, Stampede3 Tool Containerization Computer & Information Sciences Charliecloud provides user-defined software stacks (UDSS) for high-performance computing (HPC) centers.
Description Source: https://hpc.github.io/charliecloud/
Lightweight & Secure Container Tool, User-Defined Software Stacks, No Privileged Operations Or Daemons, Runs In User Space Containerization, Software Development, Research Tools https://github.com/hpc/charliecloud https://hpc.github.io/charliecloud/ https://hpc.github.io/charliecloud/tutorial.html, Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 0.33
Faster: 0.31, 0.33
Stampede-3: 0.36
Charliecloud is a software tool that provides user-defined software stacks in userspace with no privileged operations or daemons. It uses containers for software isolation and runs in user space, making it lightweight and secure.
charm Darwin Simulation Software Molecular Mechanics Force Field Biological Sciences Computational Biology, Structural Biology Bioinformatics, Biophysics 1. Simulation of proteins, nucleic acids, carbohydrates, and lipids
2. Calculation of molecular energies and forces
3. Modeling of biomolecular interactions
4. Analysis of molecular dynamics trajectories
5. Integration with various simulation packages
Molecular Mechanics, Biomolecular Simulation, Protein Structure Prediction CHARM (Chemistry at Harvard Macromolecular Mechanics) is a molecular mechanics force field for the simulation of proteins, nucleic acids, carbohydrates, and lipids. It is widely used in the field of computational biology and bioinformatics for studying the structure, dynamics, and interactions of biomolecular systems.
charmpp Expanse Charm++ is a parallel programming framework in C++ supported by an adaptive runtime system, which enhances user productivity and allows programs to run portably from small multicore computers (your laptop) to the largest supercomputers. Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Ldvm3K4, Ukcmwdo, ...
check Aces, Faster Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught.
Description Source: https://libcheck.github.io/check/
https://libcheck.github.io/check/ https://libcheck.github.io/check/doc/doxygen/html/check_8h.html https://libcheck.github.io/check/doc/check_html/check_3.html#Tutorial Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.15.2
Faster: 0.15.2
checkm Bridges-2 Bioinformatics Tool Genomics Tool Biological Sciences Microbial Ecology Ecology CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage.
Description Source: https://github.com/Ecogenomics/CheckM/wiki/Introduction#about
Estimates Genome Completeness & Contamination, Identifies Marker Genes For Phylogenetic Analysis, Supports Analysis Of Microbial Genomes From Isolates, Single Cells, Or Metagenomes, Provides Detailed Reports & Visualizations Microbial Genomics, Genome Quality Assessment, Phylogenetic Analysis, Bioinformatics https://ecogenomics.github.io/CheckM/ https://github.com/Ecogenomics/CheckM/wiki https://github.com/Ecogenomics/CheckM/wiki/Quick-Start Bridges-2: https://www.psc.edu/resources/software/checkm Bridges-2: 1.1.3 CheckM is a software tool for assessing the quality of microbial genomes recovered from isolates, single cells, or metagenomes. It provides robust statistical evaluation of genome completeness and contamination, as well as identification of marker genes for phylogenetic placement.
checkm-genome Anvil Genome Quality Assessment Tool Bioinformatics Biological Sciences Microbial Ecology Environmental Biology Checkm-genome provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. Assessment Of Genome Completeness, Estimation Of Genome Contamination Levels, Identification Of Marker Genes & Lineage-Specific Marker Sets, Visualization Of Results & Quality Metrics Metagenomics, Microbial Ecology, Genome Quality Assessment Anvil: https://www.rcac.purdue.edu/software/checkm-genome Anvil: 1.2.0, 1.2.2 CheckM-Genome is a software tool used for assessing the quality of genomes derived from metagenome-assembled data. It provides insights into the completeness and contamination levels of bacterial and archaeal genomes, aiding in the evaluation of genome quality in microbial ecology and metagenomics studies.
chemprop Aces Bioinformatics Machine Learning Tool Chemical Sciences Chemprop is a message passing neural network for molecular property prediction.
Description Source: https://chemprop.readthedocs.io/en/latest/
Deep Learning-Based Molecular Property Prediction, Transfer Learning For Easy Application Of Pre-Trained Models, Flexible Model Architecture Customization Chemoinformatics, Molecular Property Prediction, Deep Learning https://github.com/chemprop/chemprop https://chemprop.readthedocs.io/en/latest/ https://chemprop.readthedocs.io/en/latest/tutorial.html, Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.5.2-Cuda-11.7.0 Chemprop is a deep learning-based tool for molecular property prediction. It allows users to train models to predict chemical properties and enables transfer learning to easily apply pre-trained models to new datasets.
chewbbaca Anvil Tool Bioinformatics Biological Sciences Microbial Genomics Genomics chewBBACA is a comprehensive pipeline including a set of functions for the creation and validation of whole genome and core genome MultiLocus Sequence Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast Score Ratio that can be run in multiprocessor settings and a set of functions to visualize and validate allele variation in the loci. chewBBACA performs the schema creation and allele calls on complete or draft genomes resulting from de novo assemblers. 1. Whole-genome sequence analysis
2. High-resolution microbial genotyping
3. Detection of core and accessory genome elements
4. Support for bacterial typing tasks
5. Analysis of large genomic datasets
6. Phylogenetic inference and visualization
Whole-Genome Analysis, Microbial Genotyping, Bacterial Typing, Phylogenetic Inference, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/chewbbaca Anvil: 2.8.5 ChewBBACA (Chew Sequence-Based Typing Tool) is a suite of tools specifically designed for whole-genome sequence analysis, dedicated to the provision of high-resolution sequence-based microbial genotyping.
chimerax Aces, Faster Analysis & Visualization Tool Molecular Visualization Biological Sciences Structural Biology Bioinformatics UCSF ChimeraX is the next-generation visualization program from the Resource for Biocomputing, Visualization, and Informatics at UC San Francisco, following Chimera Interactive Visualization Of Molecular Structures & Density Maps, Molecular Modeling & Analysis Tools, Integration With Various Structural Biology Data Formats, Support For Virtual Reality Visualization, Scripting Capabilities For Automation & Customization Molecular Visualization, Structural Biology, Computational Chemistry https://www.cgl.ucsf.edu/chimerax/ https://www.cgl.ucsf.edu/chimerax/docs/index.html https://www.rbvi.ucsf.edu/chimerax/tutorials.html
https://www.rbvi.ucsf.edu/chimerax/docs/videos/
https://rbvi.github.io/chimerax-recipes/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.3, 1.6.1, 1.7.1
Faster: 1.2.5, 1.4, 1.5, 1.6.1, 1.7
ChimeraX is a software tool for the visualization and analysis of molecular structures, density maps, and related data. It is widely used in the field of structural biology and computational chemistry for studying complex biomolecular systems.
chopper Anvil Bioinformatics Tool Sequence Analysis Tool Biological Sciences Ngs Data Analysis Bioinformatics Chopper is Rust implementation of NanoFilt+NanoLyse, both originally written in Python. Adapter Sequence Removal, Preprocessing Of Raw Sequencing Data, Quality Control, High-Throughput Sequencing Support Bioinformatics, Ngs Data Analysis, Sequence Trimming, High-Throughput Sequencing Anvil: https://www.rcac.purdue.edu/software/chopper Anvil: 0.2.0 Chopper is a tool designed for efficient removal of adapter sequences from high-throughput sequencing data. It helps in preprocessing raw sequencing reads by trimming adapter sequences to ensure high-quality downstream analysis.
chromap Anvil Bioinformatics Analysis Tool Biological Sciences Epigenetics Genomics Chromap is an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Integrative Analysis Of Chromatin Modifications, Multi-Sample Chip-Seq Experiment Analysis, Statistical Analysis Of Chip-Seq Data, Visualization Of Chromatin Modification Patterns Chromatin Modifications, Computational Biology, Bioinformatics, Genomics Anvil: https://www.rcac.purdue.edu/software/chromap Anvil: 0.2.2 Chromap is a computational tool for comprehensive and integrative analysis of chromatin modifications from multiple ChIP-seq experiments.
cicero Anvil Text Analysis Tool Computational Software Computer & Information Sciences CICERO (Clipped-reads Extended for RNA Optimization) is an assembly-based algorithm to detect diverse classes of driver gene fusions from RNA-seq. Cicero provides tools for sentiment analysis, entity recognition, keyword extraction, text summarization, and language translation. It is designed to assist in extracting insights, trends, and patterns from large volumes of unstructured text data. Text Analysis, Natural Language Processing Anvil: https://www.rcac.purdue.edu/software/cicero Anvil: 1.8.1 Cicero is a platform for automated text analysis and natural language processing.
cimfomfa Aces This library supports both MCL, a cluster algorithm for graphs, and zoem, a macro/DSL language. It supplies abstractions for memory management, I/O, associative arrays, strings, heaps, and a few other things. The string library has had heavy testing as part of zoem. Aces: https://hprc.tamu.edu/software/aces/ Aces: 22.273
circexplorer2 Anvil Bioinformatics Tool RNA Analysis Tool Biological Sciences Transcriptomics Molecular Biology CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. It is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization. 1. Detection of circular RNA events from RNA-seq data.
2. Quantification of circRNA expression levels.
3. Visualization of circRNA back-splicing junctions and expression profiles.
4. Differential expression analysis of circRNAs between conditions.
5. Integration with other analysis tools for comprehensive circRNA studies.
Circular RNA, RNA-Seq, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/circexplorer2 Anvil: 2.3.8 Circexplorer2 is a computational tool for identifying circular RNA (circRNA) from RNA-seq data. It supports the discovery, quantification, and visualization of circRNAs in a variety of biological samples.
circlator Anvil Assembly Tools Genome Tools Biological Sciences Genome Assembly Genomics Circlator is a tool to circularize genome assemblies. Circularizing Genome Assemblies, Fixing Misassemblies, Improving Assembly Quality, Visualizing Genome Assemblies Genome Assembly, Bioinformatics, Genome Visualization, Assembly Improvement Anvil: https://www.rcac.purdue.edu/software/circlator Anvil: 1.5.5 Circlator is a tool designed for circularizing and visualizing genome assemblies, specifically for circularizing genomes, fixing misassemblies, and improving the overall assembly quality.
circompara2 Anvil Tool Bioinformatics Biological Sciences Comparative Genomics Genomics CirComPara2 is a computational pipeline to detect, quantify, and correlate expression of linear and circular RNAs from RNA-seq data that combines multiple circRNA-detection methods. Features of circompara2 include circular genome visualization, comparative genomics analysis, identification of genomic rearrangements, annotation comparison, and gene synteny analysis. Genomics, Comparative Genomics, Genome Visualization, Gene Synteny Anvil: https://www.rcac.purdue.edu/software/circompara2 Anvil: 0.1.2.1 circompara2 is a tool for circular comparison of genomes. It allows for the visualization and comparison of genomic sequences in a circular representation, enabling the identification of similarities and differences between genomes.
circos Anvil, Bridges-2 Visualization Tool Data Visualization Biological Sciences Genomics Bioinformatics Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.
Description Source: https://circos.ca/
Circular Layout Visualization, Highly Customizable Graphics, Support For Large Datasets, Integration Of Multiple Data Types, Publication-Quality Images Data Visualization, Genomics, Biological Sciences, Circular Layout https://circos.ca/ https://circos.ca/documentation/ https://circos.ca/documentation/course/
https://circos.ca/tutorials/
https://circos.ca/documentation/images/small/
Anvil: https://www.rcac.purdue.edu/software/circos
Bridges-2: https://www.psc.edu/resources/software/circos
Anvil: 0.69.8
Bridges-2: 0.69-9
Circos is a software package for visualizing data in a circular layout. It is widely used in genomics and other biological sciences to create visual representations of complex datasets.
ciri2 Anvil Analysis Tool Bioinformatics Tool Biological Sciences Molecular Biology Genetics CIRI2: Circular RNA identification based on multiple seed matching 1. Detection of circRNAs: CIRI2 employs an algorithm that utilizes back-spliced reads to detect circRNAs within RNA-Seq data.
2. High accuracy: The tool integrates multiple strategies to enhance the accuracy of circRNA identification.
3. Multiple-file input: CIRI2 supports the analysis of multiple RNA-Seq samples simultaneously.
4. Visualization capabilities: Users can visualize the identified circRNAs and their characteristics through graphical outputs.
5. Customizable parameters: The tool offers flexibility in adjusting parameters based on user requirements.
Bioinformatics, Computational Biology, RNA-Seq, Circular RNA Anvil: https://www.rcac.purdue.edu/software/ciri2 Anvil: 2.0.6 CIRI2 (CircRNA Identifier 2) is a comprehensive computational tool designed to efficiently and accurately identify circular RNAs (circRNAs) from high-throughput sequencing data. CircRNAs are a type of non-coding RNA with crucial functions in gene regulation and various biological processes.
ciriquant Anvil Ciriquant is a comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. 1. Detection of circadian rhythms in time-course gene expression data. 2. Estimation of circadian parameters such as period and phase. 3. Statistical analysis to determine significantly rhythmic genes. 4. Visualization tools for circadian patterns. Computational Biology, Time-Series Analysis, Biological Rhythms Anvil: https://www.rcac.purdue.edu/software/ciriquant Anvil: 1.1.2 ciriquant is a computational software package for analyzing circadian oscillations in time-course data. It allows for the identification of significantly rhythmic genes and estimation of circadian parameters.
cistem Aces, Faster Bioinformatics Tool Prediction Software Biological Sciences Computational Biology Bioinformatics cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
Description Source: https://cistem.org/
CISTEM uses a double-layered classification system that combines features from primary sequence and secondary structure contexts to predict accurate RNA secondary structures. Computational Framework, RNA Secondary Structures Prediction https://cistem.org/ https://cistem.org/documentation https://cistem.org/sites/default/files/uploads/cisTEM_tutorial.pdf Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.0-Beta-Linux64
Faster: 1.0.0-Beta
CISTEM is a computational framework designed for the prediction of dual phase RNA secondary structures.
ckdmip Aces Hpc Tool Computational Software Physical Sciences Cosmology Astronomy & Planetary Sciences Software for the Correlated K-Distribution Model Intercomparison Project (CKDMIP). CKDmip allows for the calculation of Cl's due to cosmic microwave background using CMB perturbation code, facilitating research and analysis in cosmology. Cosmic Microwave Background, Cmb Radiation, Temperature Anisotropies, Polarization Spectra Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.0 CKDmip is a software for computing cosmic microwave background (CMB) radiation temperature anisotropies and polarization spectra using the Cosmic Microwave Background (CMB) perturbation code.
clair3 Anvil Variant Caller Genomic Analysis Tool Biological Sciences Clair3 is a germline small variant caller for long-reads. Variant Calling For Illumina Deep Sequencing Data, Detection Of Germline & Somatic Variants, Scalable & Efficient Performance Variant Calling, Illumina, Sequencing Data Anvil: https://www.rcac.purdue.edu/software/clair3 Anvil: 0.1-R11, 0.1-R12 Clair3 is a variant caller for Illumina deep sequencing data. It is designed to detect germline and somatic variants in a flexible, scalable, and efficient manner.
clairvoyante Anvil Command Line Tool Data Analysis Biological Sciences Bioinformatics Genetics Clairvoyante is a deep neural network based variant caller. It utilizes a deep neural network model for variant calling and can accurately predict the accuracy of variant calls made by different variant calling tools. The software identifies mislabeled pronouns and suffixes, improving the accuracy of variant prediction. Variant Calling, Deep Learning, Accuracy Prediction Anvil: https://www.rcac.purdue.edu/software/clairvoyante Anvil: 1.02 clairvoyante is a deep learning-based tool for the prediction of variant calling accuracy.
clang Aces, Faster Development Tool Compiler Computer & Information Sciences Programming Languages & Compilers Software Engineering, Systems, & Development The Clang project provides a language front-end and tooling infrastructure (its a compier) for languages in the C language family (C, C++, Objective C/C++, OpenCL, CUDA, and RenderScript) for the LLVM project.
Description Source: https://clang.llvm.org/
Support For C, C++, & Objective-C Languages, Highly Optimized Code Generation Using Llvm Back End, Fast Compilation Times, Expressive Diagnostics For Easy Debugging, Modular Architecture For Easy Integration With Other Tools & Libraries Compiler, Software Development, Programming Languages https://clang.llvm.org/ https://clang.llvm.org/doxygen/index.html https://clang.llvm.org/docs/UsersManual.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 13.0.1, 15.0.5, 16.0.6
Faster: 11.0.1, 12.0.1, 13.0.1-Cuda-11.4.1, 13.0.1, 16.0.6
Clang is a compiler front end for the C, C++, and Objective-C programming languages. It uses LLVM as its back end, providing highly optimized code generation. Clang is designed to provide fast compiles, expressive diagnostics, and a modular architecture for easy integration with other tools and libraries.
clang-aomp Faster Compiler Development Tools Engineering & Technology Integration Of Amd Optimizing Compiler, Openmp Support, Optimizations For Amd Gpus Compiler, Openmp, Gpu Acceleration Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.5.0 clang-aomp is a compiler based on Clang that integrates the AMD Optimizing Compiler (AOCC) and OpenMP runtime. It is designed for accelerating applications on AMD GPUs.
clck Kyric https://www.intel.com/content/www/us/en/developer/tools/oneapi/cluster-checker.html#gs.5j2g84 https://www.intel.com/content/www/us/en/developer/tools/oneapi/cluster-checker-documentation.html https://www.intel.com/content/www/us/en/docs/cluster-checker/user-guide/2021-7-2/getting-started.html Kyric: Latest, 2021.1.1
clearcnv Anvil Bioinformatics Tool Genomic Analysis Tool Biological Sciences Genomic Variations Genomics ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise. Copy Number Variation (Cnv) Detection, Whole-Exome Sequencing (Wes) Data Analysis, Bayesian Model-Based Approach, High Sensitivity & Specificity Cnv Detection, Genomic Analysis, Sequencing Data Analysis Anvil: https://www.rcac.purdue.edu/software/clearcnv Anvil: 0.306 ClearCNV is a software tool designed for accurate copy number variation (CNV) detection from whole-exome sequencing (WES) data. It employs a Bayesian model-based approach to identify CNVs with high sensitivity and specificity.
clever-toolkit Anvil Clever-toolkit is a collection of tools to discover and genotype structural variations in genomes from paired-end sequencing reads. The main software is written in C++ with some auxiliary scripts in Python. Anvil: https://www.rcac.purdue.edu/software/clever-toolkit Anvil: 2.4
clhep Aces, Faster Computational Tool Library Physical Sciences High Energy Physics Physics 1. Vector and matrix classes
2. Random number generators
3. Physical constants and units
4. Geometry and kinematics classes
5. Reference counting and smart pointers
6. Event data model classes
C++ Library, High Energy Physics, Hep Applications Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.4.6.2
Faster: 2.4.5.1, 2.4.6.4
CLHEP (Class Library for High Energy Physics) is a library of C++ classes specifically designed for high energy physics (HEP) applications. It provides a set of utility classes for HEP-specific tasks, such as vectors, matrices, random number generation, and units of measurement.
climetlab Aces Library Data Analysis & Visualization Earth & Environmental Sciences Climate & Global Dynamics Earth & Environmental Sciences CliMetLab is a Python package aiming at simplifying access to climate and meteorological datasets, allowing users to focus on science instead of technical issues such as data access and data formats.
Description Source: https://climetlab.readthedocs.io/en/latest/index.html
Accessing Climate Datasets, Manipulating Climate Data, Visualizing Climate Data, Convenient Data Exploration Tools Python Library, Climate Data, Data Visualization https://github.com/ecmwf/climetlab https://climetlab.readthedocs.io/en/latest/ https://climetlab.readthedocs.io/en/latest/firststeps.html Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.12.6 climetlab is a Python library designed for easy access, manipulation, and visualization of climate data. It aims to simplify the process of working with climate datasets by providing a unified interface and tools for data exploration.
clip Aces Deep Learning Machine Learning Framework Computer & Information Sciences Natural Language Processing Artificial Intelligence & Intelligent Systems CLIP (Contrastive Language-Image Pre-Training) is a neural network trained on a variety of (image, text) pairs. It can be instructed in natural language to predict the most relevant text snippet, given an image, without directly optimizing for the task, similarly to the zero-shot capabilities of GPT-2 and 3.
Description Source: https://github.com/openai/CLIP
1. Pretraining on large-scale image-text datasets
2. Learning joint representations of images and text
3. Enhancing visual-linguistic understanding
4. Facilitating downstream tasks such as zero-shot learning, image-text retrieval, and visual question answering
Machine Learning, Deep Learning, Image-Text Representation, Pretraining https://openai.com/research/clip https://github.com/openai/CLIP/blob/main/notebooks/Interacting_with_CLIP.ipynb https://github.com/openai/CLIP#usage Aces: https://hprc.tamu.edu/software/aces/ Aces: 20230220-Cuda-11.7.0 CLIP (Contrastive Language-Image Pretraining) is a framework for learning joint representations of images and text. It is designed to pretrain on large scale image-text datasets to learn a powerful visual-linguistic understanding.
clonalframeml Anvil Biological Sciences ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes. 1. Inference of recombination events in bacterial and archaeal genomes. 2. Reconstruction of clonal relationships between individuals. 3. Maximum likelihood framework for accurate estimation. Bioinformatics, Hpc Tools Anvil: https://www.rcac.purdue.edu/software/clonalframeml Anvil: 1.11 ClonalFrameML is a software for inferring recombination in bacterial and archaeal genomes. It uses a maximum likelihood framework to detect recombination events and reconstruct the clonal relationships between individuals.
clp Faster Solver Optimization Software Engineering & Technology Operations Research, Industrial Engineering Standalone Linear Programming Solver, Framework For Building Custom Optimization Algorithms, Efficient Solution Of Large-Scale Linear Programming Problems Linear Programming, Optimization, Large-Scale Problems, Open-Source Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.17.7 CLP (Cbc, Lapack, and ParallelCbc) is an open-source linear programming solver that provides both a standalone solver and a framework for building custom optimization algorithms. It is designed to solve large-scale linear programming problems efficiently and offers a range of features for linear optimization.
clust Anvil Data Analysis Tool Clustering Software Other Computer & Information Sciences Clust is a fully automated method for identification of clusters (groups) of genes that are consistently co-expressed (well-correlated) in one or more heterogeneous datasets from one or multiple species. 1. Clustering heterogeneous time series data
2. Identifying similarity patterns among time series
3. Grouping time series data based on specified criteria
4. Analyzing patterns and trends within clusters
Clustering, Time Series Data, Pattern Identification Anvil: https://www.rcac.purdue.edu/software/clust Anvil: 1.17.0 Clust is a software for clustering heterogeneous time series data. It allows users to identify similarity patterns and group time series data together based on various criteria.
clustalw Anvil Tool Computational Software Biological Sciences Clustalw is a general purpose multiple alignment program for DNA or proteins. 1. Multiple sequence alignment for DNA or protein sequences
2. Identifies homologous regions and conserved motifs
3. Supports various alignment algorithms
4. Generates phylogenetic trees based on aligned sequences
Bioinformatics, Sequence Alignment Anvil: https://www.rcac.purdue.edu/software/clustalw Anvil: 2.1 ClustalW is a widely used multiple sequence alignment program for DNA or protein sequences. It aligns multiple sequences using various algorithms to identify homologous regions and conserved motifs.
clustalw2 Faster Alignment Tool Bioinformatics Biological Sciences Multiple Sequence Alignment For DNA Or Proteins, Phylogenetic Tree Generation, Visualization Of Alignments, Alignment Quality & Reliability Analysis Bioinformatics, Computational Biology, Sequence Analysis Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.1 ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences.
cluster-tools Ookami https://github.com/constantinpape/cluster_tools https://github.com/constantinpape/cluster_tools/blob/master/cluster_tools/workflows.py https://github.com/constantinpape/cluster_tools/tree/master/example Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 9.0
cm-pmix3 Expanse, Ookami System & Process Management Library Engineering & Technology Infrastructure & Instrumentation Other Computer & Information Sciences It offers capabilities for process monitoring, reporting, and control, with support for spawning, killing, and monitoring individual processes within a job. The library is designed to work seamlessly with various job schedulers and resource managers. Process Management, High-Performance Computing, Job Scheduling https://pmix.github.io/standard https://pmix.github.io/uploads/2019/02/pmix-standard-3.1.pdf https://openpmix.github.io/support/how-to/ Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Expanse: 3.1.7
Ookami: 3.1.4
cm-pmix3 is a lightweight, high-performance library that provides process management and control functions for large-scale computing environments.
cmake Aces, Anvil, Darwin, Delta, Expanse, Faster, Kyric, Ookami, Stampede3 Developer Tools Build Automation Tools Engineering & Technology Software Development Software Engineering, Systems, & Development CMake is the de-facto standard for building C++ code, with over 2 million downloads a month. It’s a powerful, comprehensive solution for managing the software build process.
Description Source: https://cmake.org/
1. Cross-platform build system
2. Automated dependency resolution
3. Package generation for multiple platforms
4. Integrated support for popular development environments
5. Extensible through custom modules
6. Supports in-place and out-of-place builds
7. Versatile project configuration options
Build System, Cross-Platform, Software Development https://cmake.org/ https://cmake.org/cmake/help/latest/ https://cmake.org/getting-started/, https://cmake.org/cmake/help/latest/guide/tutorial/index.html
https://www.youtube.com/watch?v=wl2Srog-j7I
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cmake
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 3.18.4, 3.20.1, 3.21.1, 3.22.1, 3.23.1, 3.24.3, 3.26.3, 3.27.6
Anvil: 3.20.0
Delta: 3.20.2, 3.27.9
Expanse: Bpzre3Q, Rc2Aosa, ...
Faster: 3.11.4, 3.15.3, 3.16.4, 3.18.4, 3.20.1, 3.21.1, 3.22.1, 3.23.1, 3.24.3, 3.26.3, 3.27.6
Kyric: 3.16.2
Ookami: 3.25.2
Stampede-3: 3.28.1, 3.29.5
CMake is an open-source, cross-platform family of tools designed to build, test, and package software. It is used to control the software compilation process using simple platform and compiler-independent configuration files.
cmd Ookami Framework Development Tools Computer & Information Sciences 1. Enables creation of command-line interfaces. 2. Supports the definition of commands and functions. 3. Facilitates interactive sessions. 4. Provides a customizable prompt. 5. Allows command completion and history functionality. Command Line, Python Module https://docs.nvidia.com/dgx-superpod/administration-guide-dgx-superpod/latest/cluster-management-daemon.html# https://support.brightcomputing.com/manuals/9.2/developer-manual.pdf https://www.hpe.com/psnow/resources/ebooks/a00113955en_us_v2/Manage_an_HSM_System_with_Bright.html Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: Cmd The cmd module in Python provides a framework for building interactive command line applications. It allows developers to easily create command-line interfaces by defining a set of commands and their associated functions.
cmjob Expanse, Ookami Automates Job Submissions On Hpc Clusters, Monitors Job Statuses, Organizes Job Outputs, Facilitates Management Of Multiple Computational Jobs Hpc, Computational Materials Science, Python Library https://docs.nvidia.com/dgx-superpod/administration-guide-dgx-superpod/latest/cluster-management-daemon.html# https://support.brightcomputing.com/manuals/9.2/developer-manual.pdf https://www.hpe.com/psnow/resources/ebooks/a00113955en_us_v2/Manage_an_HSM_System_with_Bright.html Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Expanse: Cmjob
Ookami: Cmjob
cmjob is a Python-based tool for computational materials science that aids in automating the submission of multiple jobs on high-performance computing clusters. It simplifies the process of handling multiple job submissions, tracking job statuses, and organizing job outputs.
cnvkit Anvil Analysis Tool Genomics Biological Sciences Molecular Biology Genetics CNVkit is a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. Detection & Genotyping Of Copy Number Variations (Cnvs), Handling Shallow Coverage Whole-Exome & Panel Target Sequencing Data, Analysis Of Tumor-Normal Pairs Bioinformatics, Hpc Tools, Computational Software Anvil: https://www.rcac.purdue.edu/software/cnvkit Anvil: 0.9.9-Py CNVkit is a software toolkit for copy number variation (CNV) detection and genotyping from targeted DNA sequencing data. It is designed to handle shallow coverage whole-exome and panel target sequencing from tumor-normal pairs.
cnvnator Anvil, Faster Tool Bioinformatics Biological Sciences Structural Genomics Genetics Cnvnator is a tool for discovery and characterization of copy number variation (CNV) in population genome sequencing data. Detection Of Copy Number Variations (Cnvs), Genotyping, Utilizes Whole-Genome Sequencing Data, Identification Of Structural Variations In The Genome Cnv Detection, Whole-Genome Sequencing, Genotyping, Structural Variations Anvil: https://www.rcac.purdue.edu/software/cnvnator
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 0.4.1
Faster: 0.4.1
CNVnator is a tool designed for the detection of copy number variations (CNVs) and genotyping using whole-genome sequencing data. It is particularly useful in studying structural variations in the human genome.
cobaya Faster Analysis Computational Tool Physical Sciences Cosmology Astronomy & Planetary Sciences Bayesian Analysis Of Physical & Cosmological Models, User-Friendly Model Definition Interface, Parameter Estimation & Sampling From Posterior Distributions Bayesian Analysis, Physical Models, Cosmological Models Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.2.2 Cobaya is an open-source platform for Bayesian analysis of physical and cosmological models. It provides a user-friendly interface for defining models, running parameter estimation, and sampling from posterior distributions.
code-server Faster Development Tool Integrated Development Environment (Ide) Computer & Information Sciences Remote Development In The Browser, Access To Visual Studio Code Environment, Real-Time Collaboration Features, Support For Extensions & Plugins, Integrated Terminal For Running Commands Remote Development, Visual Studio Code, Browser-Based Coding, Collaboration, Coding Environment Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.5.1, 4.8.3, 4.9.1, 4.19.1 Code-server is a tool that allows you to run a Visual Studio Code instance in the browser, making it convenient for remote development, collaboration, and accessing your coding environment from anywhere.
coinfinder Anvil Search Tool Image Recognition Engineering & Technology Image Processing Other Coinfinder is an algorithm and software tool that detects genes which associate and dissociate with other genes more often than expected by chance in pangenomes. Image Analysis For Coin Recognition, Search Functionality For Locating Specific Coins, User-Friendly Interface For Ease Of Use Image Analysis, Coin Recognition, Search Tool Anvil: https://www.rcac.purdue.edu/software/coinfinder Anvil: 1.2.0 CoinFinder is a software tool designed for locating specific coins in large image datasets. It provides a user-friendly interface for efficiently searching and identifying coins based on their features.
coinutils Faster Optimization Software Library Mathematics Optimization Applied Mathematics CoinUtils is an open-source collection of classes and helper functions that are generally useful to multiple COIN-OR projects. The project includes classes for storing and manipulating sparse matrices and vectors, performing matrix factorization, parsing input files in standard formats, building representations of mathematical programs, comparing floating point numbers with a tolerance, etc.
Description Source: https://www.coin-or.org/projects/#ffs-tabbed-12
1. Linear and integer programming utilities
2. LP and MIP file format conversion tools
3. Mathematical programming libraries for optimization
4. Compatible with other COIN-OR packages like Clp and Cbc
Optimization, Operations Research, Mathematical Programming https://github.com/coin-or/CoinUtils https://coin-or.github.io/CoinUtils/Doxygen/index.html https://coin-or.github.io/user_introduction.html Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.11.6 CoinUtils is an open-source C++ library that provides utilities and tools for optimization problems. It is part of the COIN-OR project, a collection of operations research software tools.
colabfold Aces, Faster Protein Structure Prediction Tool Web-Based Tool Biological Sciences Protein Structure Prediction Bioinformatics ColabFold is a web-based tool that leverages artificial intelligence to predict protein structures rapidly and accurately, making cutting-edge protein folding accessible to researchers without requiring extensive computational resources. It builds on the technology of AlphaFold by DeepMind, providing a user-friendly platform for scientific exploration and discovery in the field of bioinformatics and structural biology. Combines Deep Learning & Biophysical Modeling, Protein Structure Prediction, User-Friendly Interface Protein Structure Prediction, Deep Learning, Biophysical Modeling https://github.com/sokrypton/ColabFold https://github.com/sokrypton/ColabFold/wiki https://docs.google.com/presentation/d/1mnffk23ev2QMDzGZ5w1skXEadTe54l8-Uei6ACce8eI/edit#slide=id.p
https://www.youtube.com/watch?v=Rfw7thgGTwI
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.5.2-Cuda-11.7.0
Faster: 1.3.0-Cuda-11.3.1
ColabFold is a collaborative project that aims to bring together deep learning and biophysical modeling for protein structure prediction. It provides an easy-to-use interface for researchers to perform protein folding predictions using state-of-the-art techniques.
colossal-ai Faster Library Machine Learning Library Computer & Information Sciences Deep Learning Artificial Intelligence & Intelligent Systems 1. Simplified design of complex neural networks
2. Easy training and evaluation of neural network models
3. High-level interface for experimenting with different architectures and algorithms
4. Integration with popular deep learning frameworks
5. Supports distributed training for large-scale models
Deep Learning, Neural Networks, Machine Learning Faster: https://hprc.tamu.edu/software/faster/ Colossal-AI is an open-source library that simplifies the design, training, and evaluation of complex neural networks for deep learning tasks. It provides a high-level interface that allows researchers and practitioners to easily experiment with various neural network architectures and algorithms.
colossalai Faster Open Source Deep Learning Framework Computer & Information Sciences Deep Learning, Machine Learning Artificial Intelligence & Intelligent Systems 1. Large-scale distributed training capabilities
2. Efficient model serving for deployment
3. Unified platform for building and training deep learning models
4. Support for a wide range of deep learning architectures and algorithms
Deep Learning Framework, Large-Scale Training, Model Serving Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.1.8-Cuda-11.3.1, 0.1.13-Cuda-11.3.1 ColossalAI is an open-source deep learning framework that focuses on large-scale distributed training and efficient model serving. It provides a unified platform for researchers and practitioners to build, train, and deploy deep learning models at scale.
compiler Kyric Compiler Development Tools Computer & Information Sciences Translation Of High-Level Programming Languages Into Machine Language, Optimization Of Code For Better Performance, Error Checking & Debugging Capabilities, Generation Of Executable Files Compiler, Software Development, Programming Kyric: Latest, 2021.1.1 A compiler is a special program that processes statements written in a particular programming language and turns them into machine language or "code" that a computer's processor uses. It typically acts as a translator that converts high-level programming languages into machine language.
compiler-rt Kyric Library Compiler Runtime Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Runtime Support Libraries For Compiler-Generated Code, Designed For Use With The Llvm Compiler Infrastructure, Implements Runtime Parts Of Language Features Not Directly Supported By The Compiler Runtime Library, Compiler Support, Low-Level Support, Language Features Kyric: Latest, 2021.1.1 compiler-rt stands for Compiler Runtime Library. It is a collection of runtime libraries that provide low-level support for compiler-generated code. It is designed to be used with the LLVM compiler infrastructure and is commonly used in conjunction with Clang. The compiler-rt libraries implement runtime parts of the language features that are not supported directly by the compiler.
compiler-rt32 Kyric Runtime Library Development Library Computer & Information Sciences Systems Software Computer Science 1. Memory error detection using sanitizers
2. Built-in functions for optimized operations
3. Support libraries for compiler runtime functions
4. Designed for 32-bit architecture compilers
5. Integration with compiler toolchains
Compiler, Runtime Library, 32-Bit Architecture Kyric: Latest, 2021.1.1 The compiler-rt32 project is a runtime library that provides functionality for compilers in the 32-bit architecture. It includes various runtime components such as sanitizers, builtins, and support libraries for handling memory operations and error detection.
compiler32 Kyric Development Tools Compiler Computer & Information Sciences Support For Multiple Programming Languages, Optimization Techniques, Efficient Compilation Process Compiler, Software Development, Programming Kyric: Latest, 2021.1.1 compiler32 is a lightweight and efficient compiler software designed for compiling source code into executable programs. It supports various programming languages and optimization techniques to enhance the performance of the compiled code.
compress-raw-zlib Faster Compression & Decompression Library Computer & Information Sciences Key features include raw Zlib compression and decompression without any header or wrapper data, enabling direct interaction with Zlib streams. The library offers efficient compression and decompression operations for data processing. Compression, Decompression, Raw Zlib, Library Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.202 compress-raw-zlib is a raw Zlib compression and decompression library written in C for Python, providing low-level access to Zlib compression and decompression functionality.
comsol Bridges-2 Simulation Software Engineering & Technology Engineering & Technology Engineering COMSOL is an advanced simulation software that provides a finite element analysis, solver, and multiphysics simulation capabilities. It allows for the modeling of complex engineering and scientific problems involving coupled phenomena across fields like electromagnetics, mechanics, fluid dynamics, and chemical engineering, offering a versatile platform for both research and industrial applications. Multiphysics Simulations, Finite Element Analysis, Customizable Modeling Environment, Interactive Simulation Tools, Comprehensive Physics Libraries, Post-Processing Capabilities Simulation, Modeling, Physics, Engineering, Optimization https://www.comsol.com/ https://doc.comsol.com/6.2/docserver/#!/com.comsol.help.comsol/helpdesk/helpdesk.html https://www.comsol.com/support/learning-center Bridges-2: https://www.psc.edu/resources/software/comsol Bridges-2: 6.1 COMSOL is a platform for modeling and simulating physics-based systems. It offers a wide range of tools for multiphysics simulations, allowing users to analyze and optimize designs in various scientific and engineering fields.
concoct Anvil Data Analysis Tool Bioinformatics Tool Biological Sciences Metagenomics Environmental Biology Concoct is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 1. Metagenomic contig binning
2. Utilizes nucleotide composition, coverage, and linkage information
3. Supports multiple samples analysis
4. Facilitates the identification of microbial populations in environmental samples
Metagenomics, Bioinformatics, Genomics Anvil: https://www.rcac.purdue.edu/software/concoct Anvil: 1.1.0 Concoct is a software tool designed for the binning of metagenomic contigs by utilizing nucleotide composition, coverage across multiple samples, and linkage information derived from paired-end reads.
conda-env Delta Command Line Tool Package Management Computer & Information Sciences 1. Create new conda environments. 2. Export and share conda environments. 3. List existing conda environments. 4. Remove conda environments. 5. Update conda environments with new packages. Package Management, Environment Management Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: Cegan-Py3.9.18 Conda-env is a command-line tool that allows users to create, export, list, remove, and update conda environments. Conda is an open-source package management system and environment management system that runs on Windows, macOS, and Linux.
control-freec Anvil Bioinformatics Tool Genomic Analysis Tool Biological Sciences Cancer Genetics Genetics Control-freec is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Control-FREEC is able to detect copy-number alterations, loss of heterozygosity, and estimate purity, ploidy, and infer normal contamination in tumor samples. It can handle both paired and single tumor samples, and applies SNP calling using the Samtools-Bcftools package. Bioinformatics, Copy Number Variation, Whole-Genome Sequencing Anvil: https://www.rcac.purdue.edu/software/control-freec Anvil: 11.6 Control-FREEC is a tool for detection of copy-number alterations and loss of heterozygosity in whole-genome sequencing data.
cooler Anvil Bioinformatics Data Analysis & Visualization Biological Sciences Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices. 1. Processing Hi-C data
2. Normalization of chromatin interaction matrices
3. Visualization of chromatin interactions
4. Analysis and interpretation tools for Hi-C data
Computational Software, Hi-C Data Analysis, Chromatin Interaction Data Analysis Anvil: https://www.rcac.purdue.edu/software/cooler Anvil: 0.8.11 Cooler is a computational software package used for the analysis, normalization, and visualization of Hi-C and other chromatin interaction data. It provides tools for processing, exploring, and interpreting high-resolution chromatin interaction data.
coordgenlibs Aces, Faster Chemical Informatics Library Chemical Sciences This is Schrödinger, Inc's 2D coordinate generation. CoordgenLibs is a computational library used for automatically generating 2D coordinates for molecular structures, facilitating their visualization and analysis in chemical informatics and drug design applications. It is part of the Schrödinger suite, designed to produce chemically meaningful and aesthetically pleasing representations of molecules. 1. Generation of 3D coordinates for small molecules
2. Connectivity-based atom coordination
3. Geometric constraints for accurate coordinate assignment
4. Integration with various computational chemistry workflows
Computational Chemistry, 3D Coordinate Generation, Small Molecules https://github.com/schrodinger/coordgenlibs https://github.com/schrodinger/coordgenlibs/blob/master/README.md https://github.com/schrodinger/coordgenlibs/tree/master/example_dir Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.0.1
Faster: 3.0.1
CoordGenLibs is a set of computational chemistry libraries and tools for generating 3D coordinates for small molecules. It provides functions for assigning coordinates to atoms based on connectivity information and geometric constraints.
coverage Aces Tool Testing & Quality Assurance Engineering & Technology, Computer & Information Sciences, Software Engineering, Systems, & Development Measures Code Coverage To Evaluate The Effectiveness Of Test Suites, Identifies Parts Of The Code That Have Not Been Tested, Helps Developers Understand The Quality Of Their Testing Efforts, Can Be Used To Improve Test Coverage & Identify Potential Gaps In Testing Code Coverage, Testing, Software Development, Quality Assurance Aces: https://hprc.tamu.edu/software/aces/ Coverage is a tool used to measure the extent to which the source code of a program has been tested. It is often used in software development to assess the quality and thoroughness of testing by determining which parts of the code have been executed during testing.
coverm Anvil Genomic Analysis Tool Computational Tool Biological Sciences Bioinformatics Coverm is a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. Some core features of COVERM include calculating coverage and abundance metrics for genes in metagenomic data, assessing sample completeness, providing visualizations for coverage profiles, and enabling users to compare different samples. Metagenomics, Bioinformatics, Genomics Anvil: https://www.rcac.purdue.edu/software/coverm Anvil: 0.6.1 COVERM is a software tool for the analysis of metagenomic data, particularly for evaluating the coverage and abundance of genes or sequences within metagenomes.
covgen Anvil Analysis Tool Bioinformatics Tool Biological Sciences Covgen creates a target specific exome_full192.coverage.txt file required by MutSig. 1. Calculates sequencing coverage statistics
2. Visualizes coverage data in graphical format
3. Facilitates comparison of coverage between samples
4. Supports various sequencing platforms and data formats
5. Automates the process of calculating coverage metrics
6. Intuitive and user-friendly interface for ease of use
Sequencing Data Analysis, Coverage Statistics, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/covgen Anvil: 1.0.2 CovGen is a software tool designed for generating coverage statistics from sequencing data, particularly useful in the field of bioinformatics for analyzing the depth and distribution of sequencing coverage across the genome.
cp2k Aces, Anvil, Bridges-2, Expanse, Faster, Ookami, Stampede3 Molecular Simulation Computational Software Physical Sciences Condensed Matter Physics, Atomic, Molecular, & Optical Physics Physical Sciences CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
Description Source: https://www.cp2k.org/
Key features of CP2K include density functional theory (DFT) calculations, molecular dynamics simulations, efficient algorithms for large-scale parallel computations, advanced basis sets, and support for various functionals and dispersion corrections. It also offers tools for studying solvation effects, band structures, and NMR properties. Computational Chemistry, Quantum Mechanics, Molecular Dynamics https://www.cp2k.org/ https://manual.cp2k.org/trunk/ https://www.cp2k.org/exercises Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cp2k
Bridges-2: https://www.psc.edu/resources/software/cp2k
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 9.1-Lib, 9.1, 2022.1-Lib, 2022.1, 2023.1-Cuda-11.8.0, 2023.1-Lib, 2023.1-Plumed-2.9.0, 2023.1
Anvil: 8.2
Bridges-2: 7.1-Intel, 8.1-Gcc10.2.0-Openmpi4.0.5, ...
Expanse: Ub7Xgkh-Omp
Faster: 8.2, 2023.1-Cuda-11.8.0
Ookami: Gcc13.2/2024.1
Stampede-3: 2024.1.1
CP2K is an open-source quantum chemistry and solid state physics software package designed to perform atomistic simulations of solid-state, liquid, molecular, and biological systems. It can be used to study a wide range of properties, including electronic structures, molecular dynamics, and vibrational spectra.
cpe Delta, Ookami Tool Security Software Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Cray Compiling Environment (CCE) consists of compilers, libraries, and utilities that perform code analysis during compilation and automatically generate highly optimized code. Compilers support numerous command-line arguments to enable manual control over compiler behavior and optimization. Supported languages include Fortran, C and C++, and UPC (Unified Parallel C).
Description Source: https://cpe.ext.hpe.com/docs/cce/index.html
1. Standardized identification and description of software and hardware entities.
2. Facilitates interoperability between security tools and databases.
3. Assigns unique identifiers to each software, operating system, and hardware device.
4. Supports accurate and efficient information exchange in the cybersecurity domain.
Software Identification, Cybersecurity, Information Exchange https://www.hpe.com/psnow/doc/a50002303enw https://cpe.ext.hpe.com/docs/cce/index.html#cce https://cpe.ext.hpe.com/docs/guides/CPE/index_user_guides.html Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Delta: 23.09
Ookami: 23.02(Default)
CPE (Common Platform Enumeration) is a standardized method to describe and identify classes of applications, operating systems, and hardware devices in a consistent format. It provides unique identifiers for these entities to facilitate accurate and efficient information exchange between different security tools and databases.
cpe-nosve Ookami Computer & Information Sciences NOS/VE is a proprietary operating system of CDC in close relation to the well-renowned MULTICS operating system of MIT, see www.multicians.org. It is a virtual memory operating system, employing the 64-bit virtual mode of the Cyber 960 as opposed to the 60-bit real memory mode (CDC 6600/7600 mode) used by the NOS operating system. Both systems run concurrently on a single CPU.
Description Source: https://www.cray-cyber.org/old/documentation/nosve_howto.php
1: Utilizes canonical polyadic decomposition (CPD) analysis for network structure inference 2: Validates and elucidates complex network structures, 3: Assists in understanding the underlying architecture of networks from observed data Computational Software, Network Analysis, Data Validation, Structure Elucidation https://www.cray-cyber.org/old/documentation/nosve_howto.php https://www.cray-cyber.org/old/documentation/nosve_howto.php https://cray-cyber.org/old/systems/cy960_shortguide.php Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 21.03 CPE-NOsvE (Canonical Polyadic Decomposition-based Network Observation for Structure Validation and Elucidation) is a computational tool for network structure elucidation and validation using canonical polyadic decomposition (CPD) analysis. It is designed to infer the underlying structure of complex networks from observed data, helping researchers better understand and validate network architectures.
cppunit Faster Library Testing Framework Computer & Information Sciences Supports Test Fixtures, Test Suites, Assertions, Test Runners, Output Validation Unit Testing, C++ Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.15.1 CppUnit is a C++ unit testing framework designed to assist in writing and running automated test suites for C++ code. It is based on the xUnit architecture and is similar in functionality to JUnit for Java.
cppy Aces, Faster Integration Tool Software Library Computer & Information Sciences A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.
Description Source: https://github.com/nucleic/cppy
Embed Python Interpreter In C++ Applications, Call Python Functions From C++ Code, Exchange Data Between C++ & Python Seamlessly C++, Python, Embedded Python, Interoperability https://github.com/nucleic/cppy https://cppy.readthedocs.io/en/latest/ https://cppy.readthedocs.io/en/latest/installation.html#using-cppy-in-an-extensions Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.1.0, 1.2.1
Faster: 1.1.0, 1.2.1
C++ embedded Python library to seamlessly interact with C++ and Python code within the same application.
cpu Expanse Component Hardware Computer & Information Sciences 1. Executes instructions from computer programs
2. Performs arithmetic and logic operations
3. Manages data and input/output operations
4. Controls other hardware components
5. Supports multitasking and multiprocessing
Hardware, Computing, Technology Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 0.15.4, 0.17.3B CPU (Central Processing Unit) is a hardware component of a computer that executes instructions and performs calculations. It is considered the brain of the computer and is responsible for carrying out tasks and running applications.
cramino Anvil Scientific Software Simulation Software Chemical Sciences Chemical Sciences Physical Sciences Cramino is a tool for quick quality assessment of cram and bam files, intended for long read sequencing. Molecular dynamics simulations, Quantum chemistry calculations, Energy minimization, Molecular visualization, Trajectory analysis Computational Chemistry, Molecular Dynamics, Quantum Chemistry Anvil: https://www.rcac.purdue.edu/software/cramino Anvil: 0.9.6 Cramino is a software tool designed for computational chemistry simulations and molecular dynamics studies.
cray Delta Hpc Tool Computational Software Computer & Information Sciences 1. High-performance computing capabilities
2. Scalability to handle massive workloads
3. Advanced parallel processing architecture
4. Support for various scientific and engineering applications
5. Efficient use of compute resources
Supercomputing, High-Performance Computing, Scientific Computing Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Cray is a supercomputing company well-known for its high-performance computing systems and solutions. Cray supercomputers are designed to handle complex computational tasks and large-scale scientific simulations.
crisprcasfinder Anvil Genome Analysis Tool Bioinformatics Tool Biological Sciences Bioinformatics Genetics Crisprcasfinder is an updated, improved, and integrated version of CRISPRFinder and CasFinder. 1. Detection of CRISPR arrays in bacterial and archaeal genomes. 2. Identification of Cas proteins associated with CRISPR loci. 3. Prediction of potential CRISPR-Cas systems configurations. 4. Visualization of CRISPR arrays and Cas proteins in genomic context. Genome Analysis, Crispr-Cas Systems, Prokaryotic Genomes Anvil: https://www.rcac.purdue.edu/software/crisprcasfinder Anvil: 4.2.20 CRISPRCasFinder is a tool for the identification of CRISPR arrays and Cas proteins in prokaryotic genomes. It uses a combination of CRISPR technology and Cas protein identification to accurately identify CRISPR-Cas systems in bacterial and archaeal genomes.
crispresso2 Anvil Analysis Tool Bioinformatics Biological Sciences Molecular Biology, Genetics Biochemistry & Molecular Biology, Genetics CRISPResso2 is a software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Quantification Of Editing Efficiency, Visualization Of Editing Patterns, Assessment Of Indel Formation & Repair Mechanisms, Identification Of Off-Target Effects Crispr, Genome Editing, Sequencing Data Analysis Anvil: https://www.rcac.purdue.edu/software/crispresso2 Anvil: 2.2.8, 2.2.9, 2.2.10, 2.2.11A CRISPResso2 is a software tool for the analysis of CRISPR-Cas9 genome editing outcomes from deep sequencing data. It provides researchers with a comprehensive and user-friendly platform to quantify editing efficiency, visualize editing patterns, and assess indel formation and repair mechanisms.
crispritz Anvil Web-Based Tool Bioinformatics Tool Biological Sciences Crispritz is a software package containing 5 different tools dedicated to perform predictive analysis and result assessement on CRISPR/Cas experiments. Guide RNA Design For Gene Knockout, Guide RNA Design For Gene Editing, Guide RNA Design For Transcriptional Activation, High Specificity & Efficiency, Web-Based Interface Crispr/Cas9, Guide RNA Design, Genome Editing, Molecular Biology Anvil: https://www.rcac.purdue.edu/software/crispritz Anvil: 2.6.5 CRISPRitz is a web-based software tool for designing and analyzing CRISPR/Cas9 guide RNAs. It allows users to design guide RNAs for gene knockout, gene editing, and transcriptional activation with high specificity and efficiency.
cross_match Anvil Matching Tool Data Processing Physical Sciences Astronomy Astronomy & Planetary Sciences cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Alignment Of Two Lists Of Objects, Identification Of Matching Entries, Astronomical Applications, Handling Of Astronomical Catalog Data Alignment, Astronomy, Cataloging, Data Processing Anvil: https://www.rcac.purdue.edu/software/cross_match Anvil: 1.090518 Cross_Match is a software package used for aligning two lists of objects, usually representing detected sources or astronomical catalogs, in order to identify matching or related entries.
crossmap Anvil Bioinformatics Tool Utility Tool Biological Sciences Genome Assembly & Annotation Genomics Crossmap is a program for genome coordinates conversion between different assemblies. Conversion Of Genome Coordinates Between Different Assemblies, Mapping Of Genomic Annotations & Features, User-Friendly Interface Genome Assembly, Genomics, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/crossmap Anvil: 0.6.3 CrossMap is a versatile tool for genome coordinates conversion between different assemblies. It provides a unified and user-friendly interface for mapping features such as genomic intervals, gene coordinates, and other genomic annotations between various genome assemblies.
cryosparc Aces, Darwin Cryo-Em Software Data Processing Biological Sciences Structural Biology Biophysics Automated Particle Picking, 3D Heterogeneity Analysis, Ab-Initio 3D Reconstruction, High-Resolution Refinement, Model Building & Validation Cryo-Em, Biological Macromolecules, Structural Biology, Data Processing Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.2.1 CryoSPARC is a comprehensive software platform for cryo-EM data processing that enables high-resolution structure determination of biological macromolecules.
cryptography Aces, Faster Software Tools Computer & Information Sciences cryptography is a package designed to expose cryptographic primitives and recipes to Python developers. Encryption, decryption, secure communication, digital signatures, authentication, key generation Security, Privacy, Encryption, Decryption Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 41.0.1, 41.0.4, 41.0.5
Faster: 41.0.1
Cryptography is the practice and study of techniques for secure communication in the presence of third parties. It involves creating and analyzing protocols that prevent third parties or the public from reading private messages.
cryptsetup Kyric System Software Utility Computer & Information Sciences Disk Encryption Setup, Luks Support, Cryptographic Volume Management, Interaction With Encrypted Volumes Disk Encryption, Data Security, Cryptography, Linux https://github.com/grahamgilbert/crypt https://github.com/grahamgilbert/crypt/blob/master/README.md https://github.com/grahamgilbert/crypt/blob/master/Example%20Crypt%20Profile.mobileconfig cryptsetup is a utility used to conveniently set up disk encryption based on the Dm-crypt kernel module. It allows users to easily configure encrypted block devices using LUKS (Linux Unified Key Setup), manage cryptographic volumes, and interact with encrypted volumes.
csvkit Anvil Command-Line Tool Data Manipulation Tools Computer & Information Sciences csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 1. Convert CSV files between different formats.
2. Query CSV files using SQL.
3. Clean and manipulate CSV files.
4. Combine and merge CSV files.
5. Summarize, analyze, and visualize CSV data.
6. Work with large CSV files efficiently.
Csv, Command-Line, Data Manipulation, Data Analysis Anvil: https://www.rcac.purdue.edu/software/csvkit Anvil: 1.1.1 csvkit is a suite of command-line tools for converting and working with CSV files in various ways.
csvtk Anvil Command Line Tool Data Analysis Tool Other Computer & Information Sciences Csvtk is a cross-platform, efficient and practical CSV/TSV toolkit. Convert Between Csv & Tsv Formats, Merge Multiple Files By Rows Or Columns, Filter Rows Or Columns Based On Specified Conditions, Sort Data Based On Specified Columns, Perform Basic Statistics On Columns, Join Tables Based On Specified Keys, Extract Specific Columns Or Rows, Split Large Files Into Smaller Chunks Data Manipulation, Tabular Data, Data Analysis, Data Processing Anvil: https://www.rcac.purdue.edu/software/csvtk Anvil: 0.23.0, 0.25.0 csvtk is a cross-platform, efficient, and practical CSV/TSV toolkit for working with flat files. It aims to make it easy to work with csv and tsv data, providing a variety of functionalities for processing, cleaning, and analyzing tabular data.
cti Delta Threat Intelligence Library Computer & Information Sciences Parsing Structured Threat Intelligence Data, Manipulating Threat Intelligence Information, Support For Various Threat Intelligence Data Formats, Serialization Of Data Into Different Formats Threat Intelligence, Data Parsing, Open Source Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html CTI (Common Threat Intelligence) is an open source library designed to parse and manipulate structured threat intelligence information. It provides a set of APIs to work with different threat intelligence data formats and supports the serialization of data into various formats.
cubegui Aces Graphical User Interface (Gui) Data Visualization Natural Sciences Physical Chemistry Chemical Sciences Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer. Cubegui allows users to load, visualize, and manipulate volumetric data files in various formats. It provides tools for interactive exploration of molecular and crystal structures, electron densities, molecular orbitals, and other properties derived from quantum mechanical calculations. Users can customize visual representations, create animations, and perform analysis on the volumetric data. Gui Software, Volumetric Data Visualization, Computational Chemistry, Materials Science Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.8.2 Cubegui is a graphical user interface (GUI) software designed for visualizing and analyzing volumetric data in computational chemistry and materials science.
cubelib Aces Computational Software Library Computer & Information Sciences Parallel Computing Computer Science Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools. cubelib provides efficient implementations of parallel reduction operations such as sum, min, max, and custom-defined reduction operators on multi-dimensional arrays. It is optimized for CUDA-enabled GPUs and supports various data types and reduction strategies for improved performance. Software Library, C++, Cuda, Parallel Computing, Multi-Dimensional Arrays Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.8.1, 4.8.2 cubelib is a C++ library for parallel reduction operations on multi-dimensional arrays using CUDA.
cubewriter Aces Productivity Tool Research & Writing Tools Other Natural Sciences Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. Key features of Cubewriter include template-based formatting for various journals, real-time collaboration and feedback, references management, version control, and integration with LaTeX for advanced document customization. Scientific Writing, Document Formatting, Research Collaboration, References Management Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.8.2 Cubewriter is a software tool that enables researchers to organize, write, and format scientific papers efficiently.
cuda Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Jetstream, Ookami Compiler Development Tools Computer & Information Sciences The NVIDIA® CUDA® Toolkit provides a development environment for creating high performance GPU-accelerated applications. With the CUDA Toolkit, you can develop, optimize, and deploy your applications on GPU-accelerated embedded systems, desktop workstations, enterprise data centers, cloud-based platforms and HPC supercomputers.
Description Source: https://developer.nvidia.com/cuda-toolkit
Parallel Computing Platform, Programming Model For Nvidia Gpus, Support For C, C++, & Fortran Programming Languages, Unified Memory For Simplified Memory Management, Performance Optimization Tools Parallel Computing, Gpu Programming, High Performance Computing, Software Development https://developer.nvidia.com/cuda-zone https://docs.nvidia.com/cuda/ https://developer.nvidia.com/how-to-cuda-c-cpp
https://youtu.be/H3AQnlpxk0c
https://youtu.be/_JgNA82325I
https://youtu.be/dB5Jxwj0PDw
https://developer.nvidia.com/cuda-toolkit
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cuda
Bridges-2: https://www.psc.edu/resources/software/cuda
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 11.1.1, 11.3.1, 11.4.1, 11.7.0, 11.8.0, 12.0.0, 12.1.0, 12.1.1, 12.2.0, 12.2.2, 12.3.0, 12.3.2
Anvil: 11.0.3, 11.2.2, 11.4.2, 12.0.1
Bridges-2: 9.2.0, 10.0.0, 10.2.0, 11.7.1, 12.4.0
Delta: 11.3.1, 11.7.0, 11.8.0.Testing, 11.8.0, ...
Expanse: Blza2Ps, Ouuq5Zm
Faster: 10.1.243, 11.0.2, 11.1.1, 11.2.2, 11.3.1, 11.4.1, 11.4.2, 11.5.0, 11.6.0, 11.7.0, 11.8.0, 12.0.0, ...
Ookami: Toolkit/11.2
CUDA is a parallel computing platform and application programming interface model created by NVIDIA. It allows software developers to use a CUDA-enabled graphics processing unit for general-purpose processing.
cuda-dcgm Expanse Monitoring Tool Device Management Computer & Information Sciences Real-Time Monitoring Of Gpu Performance Metrics, Alerting & Notification Of Hardware Errors & Failures, Policy-Based Power & Temperature Management, Historical Data Collection For Analysis & Reporting Gpu Management, Monitoring, Diagnostics, Data Center, Nvidia Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 3.1.3.1 NVIDIA's Data Center GPU Manager (DCGM) is a suite of tools for managing and monitoring GPU devices in data center environments. It provides real-time monitoring, troubleshooting, and diagnostics capabilities.
cuda-quantum Anvil Quantum Computing Simulator Simulation & Modeling Computer & Information Sciences Artificial Intelligence & Intelligent Systems Computer Science Cuda-Accelerated Quantum Computing Simulator, Efficiently Simulates Quantum Circuits On Nvidia Gpus, High-Performance Platform For Simulating Large-Scale Quantum Computations, Emphasis On Speed & Scalability Quantum Computing, Cuda-Accelerated, Quantum Simulator, Nvidia Gpu, High-Performance Computing Anvil: https://www.rcac.purdue.edu/software/cuda-quantum Anvil: 0.4.0 cuda-quantum is a CUDA-accelerated quantum computing simulator designed to efficiently simulate quantum circuits on NVIDIA GPUs. It provides a high-performance platform for simulating large-scale quantum computations with a focus on speed and scalability.
cuda-samples Aces, Faster Code Sample Repository Developer Tools Computer & Information Sciences Samples for CUDA Developers which demonstrates features in CUDA Toolkit Diverse Collection Of Cuda Code Samples, Covers Various Cuda Programming Concepts & Techniques, Helps Developers Learn & Practice Gpu Programming, Provides Hands-On Examples For Cuda Programming Cuda, Gpu Programming, Code Samples, Nvidia Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 12.1-Cuda-12.1.1
Faster: 12.1-Cuda-12.1.1
cuda-samples is a collection of CUDA code samples and examples provided by NVIDIA. These samples cover a wide range of CUDA programming concepts and techniques, serving as useful resources for developers to learn and practice GPU programming using CUDA.
cuda10.2 Expanse CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Note: This package does not currently install the drivers necessary to run CUDA. These will need to be installed manually. Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 10.2.89
cuda11.7 Expanse Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 11.7.1
cudacore Aces, Faster High-Performance Computing Tool Computational Software Engineering & Technology High-Performance Computing Other Engineering & Technologies CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
Description Source: https://hprc.tamu.edu/software/aces/#
1. Utilizes GPU computing power for parallel processing
2. Supports CUDA programming model for high-performance computing
3. Accelerates complex calculations in scientific and engineering domains
4. Enhances computational efficiency and speed for diverse applications
Computational Software, Cuda, Gpu Computing, Scientific Computing, Engineering Applications https://github.com/NVIDIA/cccl https://docs.nvidia.com/cuda/cuda-c-programming-guide/ https://nvdam.widen.net/s/brxsxxtskb/dli-learning-journey-2009000-r5-web Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 11.1.1
Faster: 11.0.2, 11.1.1, 11.4.1
cudacore is a high-performance computational software that leverages GPU (Graphics Processing Unit) computing through CUDA (Compute Unified Device Architecture) for accelerated processing of scientific and engineering applications.
cudf Aces, Faster Library Data Processing & Analysis Computer & Information Sciences, Artificial Intelligence & Intelligent Systems cuDF is a GPU DataFrame library for loading joining, aggregating, filtering, and otherwise manipulating data. cuDF leverages libcudf, a blazing-fast C++/CUDA dataframe library and the Apache Arrow columnar format to provide a GPU-accelerated pandas API.
Description Source: https://github.com/rapidsai/cudf
1. Distributed DataFrames for larger-than-memory datasets
2. GPU-accelerated DataFrame operations such as sorting, filtering, joining, and aggregating
3. Easily integrates with other RAPIDS components like cuML for machine learning tasks
4. Can handle complex data operations on large datasets efficiently and effectively
5. Supports a wide variety of file formats for data ingestion and export
Dataframe, Gpu Acceleration, Data Manipulation https://github.com/rapidsai/cudf https://docs.rapids.ai/api/cudf/stable/user_guide/api_docs/ https://docs.rapids.ai/api/cudf/stable/user_guide/10min/
https://www.youtube.com/watch?v=lV7rtDW94do,
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 23.04.0, 23.08.00
Faster: 23.04.0
CUDF is part of the RAPIDS suite of open-source software libraries and APIs built on CUDA. It provides a DataFrame manipulation library leveraging GPU acceleration for loading, joining, aggregating, filtering, and otherwise manipulating tabular data.
cudnn Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster Deep Learning Accelerator Library Computer & Information Sciences Deep Learning Artificial Intelligence & Intelligent Systems The NVIDIA CUDA® Deep Neural Network (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cuDNN provides highly tuned implementations for standard routines such as forward and backward convolution, attention, matmul, pooling, and normalization.
Description Source: https://docs.nvidia.com/cudnn/index.html
1. GPU-accelerated deep neural network library
2. Optimized implementations of deep learning operations
3. Supports frameworks like TensorFlow, PyTorch, and MXNet
4. Enables faster training of deep learning models
5. Includes functions for convolution, pooling, normalization, and activation layers
Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks https://developer.nvidia.com/cudnn https://docs.nvidia.com/cudnn/index.html https://docs.nvidia.com/deeplearning/cudnn/installation/overview.html
https://docs.nvidia.com/deeplearning/cudnn/archives/cudnn_765/cudnn-developer-guide/index.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cudnn
Bridges-2: https://www.psc.edu/resources/software/cudnn
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.0.4.30-Cuda-11.1.1, 8.2.1.32-Cuda-11.3.1, 8.2.2.26-Cuda-11.4.1, 8.4.1.50-Cuda-11.7.0, 8.6.0.163-Cuda-11.8.0, ...
Anvil: Cuda-11.0_8.0, Cuda-11.2_8.1, Cuda-11.4_8.2, Cuda-12.0_8.8
Bridges-2: 8.0.4
Delta: 8.4.1.50, 8.9.0.131
Expanse: Tdvkbaf, ...
Faster: 7.6.4.38, 8.0.4.30-Cuda-11.0.2, 8.0.4.30-Cuda-11.1.1, 8.1.0.77-Cuda-11.2.2, 8.2.1.32-Cuda-11.3.1, 8.2.2.26-Cuda-11.4.1, ...
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library for deep neural networks. It provides highly optimized implementations of common deep learning operations.
cue-login-env Anvil, Delta, Expanse Python Library Development Tools Computer & Information Sciences XSEDE Operations and User Services groups recommend implementation of the cue-login-env module by SPs with XRAC allocated resources (at any SP Level). This module will provide variables containing resource information (e.g. hostname), reference location information (e.g. URLs to documentation, paths to community spaces) as well as defining the user's Home, Work & Scratch directories and other file spaces.
Description Source: https://software.xsede.org/xsede-software-and-service-component/common-user-environment-cue
Configuring User-Specific Environment Variables, Managing User-Specific Paths & Aliases, Isolating User Environments From System-Wide Configurations, Simplifying Environment Setup On Shared Servers Or Computing Clusters Python Library, User-Specific Environment, Shared Servers, Computing Clusters https://software.xsede.org/xsede-software-and-service-component/common-user-environment-cue https://hdl.handle.net/2142/75910 Anvil: https://www.rcac.purdue.edu/software/cue-login-env
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 1.1
Delta: 1.0
Expanse: Cue-Login-Env
Cue-login-env is a Python library that provides an easy way to configure user-specific environments within shared servers or computing clusters. It helps users manage their environment variables, aliases, and paths without interfering with the system-wide configurations.
cufflinks Anvil, Expanse Tool Bioinformatics Biological Sciences Sciences Biology Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Description Source: https://cole-trapnell-lab.github.io/cufflinks/
Transcript Assembly, Abundance Estimation, Differential Expression Analysis, Regulation Testing RNA-Seq, Transcriptomics, Bioinformatics https://cole-trapnell-lab.github.io/cufflinks/ https://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html https://cole-trapnell-lab.github.io/cufflinks/getting_started/ Anvil: https://www.rcac.purdue.edu/software/cufflinks
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 2.2.1
Expanse: 2.2.1
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
cunit Aces, Faster Testing Framework Testing Computer & Information Sciences Automated testing framework for C. Supports Various Assertion Styles, Test Case Management, Logging & Reporting Of Test Results, Integration With Build Systems, Extensible & Customizable For Specific Testing Needs Unit Testing, C Programming, Development Tools Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.1-3
Faster: 2.1-3
CUnit is a lightweight C unit testing framework for automated testing of C code. It provides an easy-to-use framework for writing test cases and test suites to verify the correct functioning of C programs.
cupy Aces, Faster Gpu Computing Library Computer & Information Sciences Gpu-Accelerated Computing With Python, Drop-In Replacement For Numpy, Seamless Integration With Python Libraries Python Library, Gpu Computing, Numpy Replacement Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 11.4.0-Cuda-11.4.1
Faster: 11.4.0-Cuda-11.4.1
CuPy is an open-source library that provides GPU-accelerated computing with Python. It is built as a drop-in replacement for NumPy and works seamlessly with other libraries in the Python ecosystem.
cuquantum-appliance Anvil Anvil: https://www.rcac.purdue.edu/software/cuquantum-appliance Anvil: 23.03
curl Aces, Anvil, Expanse, Faster, Kyric, Ookami Networking Tool Command-Line Tool Computer & Information Sciences, Other Computer & Information Sciences cURL is a command line tool and library for transferring data with URLs.
Description Source: https://curl.se/
Supports Various Protocols Like Http, Ftp, Scp, Sftp, Etc., Allows For Easy Transfer Of Data With Urls, Command-Line Tool For Scripting & Automation Tasks, Highly Customizable With Many Options & Configurations Networking, Data Transfer, Command-Line, Scripting https://curl.se/ https://curl.se/docs/ https://curl.se/docs/tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/curl
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 7.72.0, 7.76.0, 7.78.0, 7.83.0, 7.86.0, 8.0.1, 8.3.0
Anvil: 7.76.1
Expanse: 7.72.0
Faster: 7.60.0, 7.66.0, 7.69.1, 7.72.0, 7.76.0, 7.78.0, 7.83.0, 7.86.0, 8.0.1, 8.3.0
Ookami: 7.85.0
curl is a command-line tool and library for transferring data with URLs. It supports various protocols including HTTP, HTTPS, FTP, FTPS, SCP, SFTP, and more. It is widely used in scripting and automation tasks, as well as for debugging network issues.
cusparselt Aces, Faster Computational Software Library Computer & Information Sciences Applied Computer Science Computer Science NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in which at least one operand is a sparse matrix 1. Sparse matrix-vector multiplication (SpMV)
2. Sparse matrix solution (Ax = b) for linear systems
3. Support for various sparse matrix formats
4. GPU acceleration for faster computation
5. Integration with CUDA programming model
Sparse Matrix Operations, Gpu Acceleration, Linear Algebra, Cuda Programming Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.5.0.1-Cuda-12.2.2
Faster: 0.3.0.3-Cuda-11.4.1
CusparseLT library is a lightweight version of NVIDIA's cuSPARSE library designed for sparse matrix operations on NVIDIA GPUs. It offers high-performance accelerated computation for sparse matrix manipulation in GPU-accelerated applications.
cusz Faster Bioinformatics Data Analysis Biological Sciences Single-Cell RNA Sequencing Cell Biology CUSZ offers advanced clustering algorithms and annotation methods tailored for analyzing single-cell RNA-seq data. It can handle large datasets with efficiency and scalability while providing accurate and interpretable results. Single-Cell RNA-Seq, Clustering, Annotation Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.3.1 CUSZ is a fast and memory-efficient software tool for clustering and annotating large single-cell RNA-seq datasets.
cutadapt Aces, Anvil, Bridges-2, Faster Sequence Analysis Tool Bioinformatics Tool Biological Sciences Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. Cutadapt helps with these trimming tasks by finding the adapter or primer sequences in an error-tolerant way. It can also modify and filter single-end and paired-end reads in various ways. Adapter sequences can contain IUPAC wildcard characters. Cutadapt can also demultiplex your reads.
Description Source: https://cutadapt.readthedocs.io/en/stable/
Removes Adapter Sequences From High-Throughput Sequencing Reads, Identifies & Trims Various Types Of Unwanted Sequences, Flexibility In Specifying Adapter Sequences & Error Rates, Support For Various Sequencing Platforms Bioinformatics, Ngs, Sequence Analysis, Genomics https://github.com/marcelm/cutadapt https://cutadapt.readthedocs.io/en/stable/reference.html https://cutadapt.readthedocs.io/en/stable/guide.html
https://cutadapt.readthedocs.io/en/stable/recipes.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/cutadapt
Bridges-2: https://www.psc.edu/resources/software/cutadapt
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.5
Anvil: 2.10, 3.4, 3.7
Bridges-2: 2.10
Faster: 3.4, 3.5
cutadapt removes adapter sequences from high-throughput sequencing reads. It finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutensor Aces, Delta, Faster Computational Software Library Computer & Information Sciences High-Performance Computing (Hpc) Applied Computer Science NVIDIA cuTENSOR is a GPU-accelerated tensor linear algebra library for tensor contraction, reduction, and elementwise operations. Using cuTENSOR, applications can harness the specialized tensor cores on NVIDIA GPUs for high-performance tensor computations and accelerate deep learning training and inference, computer vision, quantum chemistry, and computational physics workloads.
Description Source: https://developer.nvidia.com/cutensor
1. Highly optimized tensor contractions
2. Element-wise operations for tensors
3. Utilizes CUDA for GPU acceleration
4. Efficient computation of large-scale tensor operations
5. Supports various tensor data types
Cuda, Gpu Acceleration, Tensor Operations, Parallel Computing https://developer.nvidia.com/cutensor https://docs.nvidia.com/cuda/cutensor/latest/api/index.html https://docs.nvidia.com/cuda/cutensor/latest/user_guide.html#user-guide-label
https://docs.nvidia.com/cuda/cutensor/latest/getting_started.html#getting-started-label
Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.6.1.5-Cuda-11.4.1, 1.6.1.5-Cuda-11.7.0, 1.7.0.1-Cuda-12.0.0
Delta: 1.5.0.3
Faster: 1.6.1.5-Cuda-11.4.1, 1.6.1.5-Cuda-11.7.0
cuTensor is a CUDA-accelerated library for tensor operations in NVIDIA GPUs. It provides optimized implementations for tensor contractions and element-wise operations, allowing for efficient computation of large-scale tensor operations in parallel.
cuttlefish Anvil Physical Sciences Cuttlefish is a fast, parallel, and very lightweight memory tool to construct the compacted de Bruijn graph from sequencing reads or reference sequences. Ray-Tracing Simulations, Modeling Optical Systems, Simulation Of Imaging Systems Software Simulation, Optical Systems, Ray Tracing Anvil: https://www.rcac.purdue.edu/software/cuttlefish Anvil: 2.1.1 Cuttlefish is a software package that enables users to efficiently simulate imaging systems in ray-tracing simulations, particularly to model the performance of optical systems.
cxxopts Stampede3 Computer & Information Sciences Provides a simple API for defining and parsing command line arguments in C++ applications. Supports a wide range of argument types, such as bool, string, integer, floating-point numbers, and custom data types. Allows specifying required arguments, default values, and help text. Enables grouping of options, subcommands, and handling positional arguments. C++, Command Line Arguments, Parsing, Library Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Stampede-3: 3.1.1, 3.2.0 A lightweight C++ library for parsing command line arguments, inspired by Python's argparse library.
cython Aces, Faster Language Compiler Compiler Computer & Information Sciences Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
Description Source: https://cython.org/
Cython allows for easy integration of C libraries and functions with Python code, enabling developers to speed up Python code by writing performance-critical portions in C. It also provides static type declarations that can lead to performance improvements over pure Python code. Programming Language, C Extensions, Python, Cython https://cython.org/ https://cython.readthedocs.io/en/latest/ https://cython.readthedocs.io/en/latest/src/tutorial/cython_tutorial.html
https://pythonprogramming.net/introduction-and-basics-cython-tutorial/
https://www.youtube.com/watch?v=JKCjsRDffXo
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.29.33, 3.0.7
Faster: 0.29.22, 0.29.30, 0.29.33, 3.0A5, 3.0.7
Cython is a programming language that makes it easy to write C extensions for Python. It provides a superset of the Python language that allows for calling C functions and declaring C types on variables and class attributes.
cython-blis Aces Library Computational Software Computer & Information Sciences Fast BLAS-like operations from Python and Cython, without the tears. This repository provides the Blis linear algebra routines as a self-contained Python C-extension.
Description Source: https://github.com/explosion/cython-blis
Provides a Cython interface for the BLIS linear algebra library, allowing for efficient linear algebra computations in Python. BLIS is a high-performance, portable, and thread-safe open-source library for linear algebraic operations. Cython, Blis, Linear Algebra, Python https://github.com/explosion/cython-blis https://github.com/explosion/cython-blis/blob/master/extra-include/configure https://github.com/explosion/cython-blis/tree/master?tab=readme-ov-file#usage Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.9.1 Cython wrapper around BLIS linear algebra library for Python.
cytoolz Faster Utility Python Library Computer & Information Sciences - High Performance Utility Functions For Iterables, Functions, & Dictionaries, - Extends The Itertools Module With Additional Functions, - Improved Performance Through Cython Optimization Python Library, Functional Programming, Utility Functions Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.9.0-Python-2.7.16, 0.12.0-Python-3.9.6 CyToolz is a "cythonized" version of the Toolz library, providing high performance utility functions for iterables, functions, and dictionaries in Python. It offers a set of functional tools for iterators that extends the itertools module with additional functions.
cyvcf2 Anvil Library Computational Biological Sciences Genomics Bioinformatics Cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files. das_t 1. Read and write VCF files efficiently.
2. Extract genetic variants and associated information.
3. Filter variants based on user-defined criteria.
4. Perform complex genomic analyses and comparisons.
5. Integrate seamlessly with other Python libraries for genomics.
Genomics, Vcf, Variant Calling, Python Anvil: https://www.rcac.purdue.edu/software/cyvcf2 Anvil: 0.30.14 CyVCF2 is a fast and efficient Python interface for reading and writing Variant Call Format (VCF) files. It provides a high-level API that simplifies the manipulation and analysis of genetic variants.
dace Faster Computer & Information Sciences 1. Support for high-dimensional and categorical data assimilation.
2. Implementation of various data assimilation algorithms.
3. Integration of observational data with models.
4. Improves predictions and understanding of complex systems.
Data Assimilation, Python Toolkit, Observational Data Integration Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.14.1 dace (Data Assimilation for Categorical and High-Dimensional Data) is a Python toolkit for data assimilation, specifically designed for high-dimensional and categorical data. It provides a range of data assimilation algorithms and tools to effectively integrate observational data and models to improve predictions and understanding of complex systems.
dal Kyric Collision Avoidance Software Library Engineering & Technology Collision Avoidance Algorithms, Robotics Applications Robotics, Collision Avoidance Kyric: Latest, 2021.1.1 DAL is a library for collision avoidance in robotics applications.
dalton Faster Simulation Quantum Chemistry Software Chemical Sciences Theoretical Chemistry Physical Chemistry Some core features of Dalton include molecular property calculations, density functional theory calculations, coupled cluster calculations, symmetry-adapted perturbation theory, and relativistic effects calculations. Quantum Chemistry, Molecular Properties, Ab Initio Calculations Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020.0 Dalton is an powerful quantum chemistry program for the study of molecular properties. It can perform a variety of high-level ab initio quantum chemical calculations for both ground and excited states.
darshan-runtime Expanse Tool Performance Analysis Computer & Information Sciences High-Performance Computing Infrastructure & Instrumentation Darshan (runtime) is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. 1. I/O access pattern analysis
2. Performance metrics collection
3. Lightweight and easy-to-use
4. Designed for HPC applications
I/O Characterization, High-Performance Computing, Performance Analysis Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 3.2.1 Darshan is a lightweight I/O characterization tool for high-performance computing (HPC) applications. It allows users to understand and improve the I/O behavior of their applications by collecting I/O access patterns and performance metrics.
darshan-util Expanse Utility Hpc Tools Physical Sciences Darshan (util) is collection of tools for parsing and summarizing log files produced by Darshan (runtime) instrumentation. This package is typically installed on systems (front-end) where you intend to analyze log files produced by Darshan (runtime). 1. Analyzing I/O behavior in HPC applications
2. Visualizing I/O patterns and bottlenecks
3. Generating reports for understanding application I/O performance
Hpc, I/O Characterization, Data Analysis Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 3.2.1 Darshan is a scalable HPC I/O characterization tool designed to capture I/O behavior in high-performance computing applications. The darshan-util package provides a set of utilities for analyzing and visualizing the I/O data collected by Darshan.
das_tool Anvil Genomic Data Analysis Tool Analysis & Visualization Biological Sciences Genomics Bioinformatics DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. Analyze Large-Scale Genomic Datasets, Visualize Chromatin Interactions, Study 3D Genome Organization, Identify Regulatory Elements, Explore Spatial Genome Architecture Genomics, Chromatin Interactions, Spatial Genome Architecture, Regulatory Elements, Bioinformatics, Data Visualization Anvil: https://www.rcac.purdue.edu/software/das_tool Anvil: 1.1.6 das_tool is a versatile software tool used for analyzing and visualizing large-scale genomic data in the context of chromatin interactions and 3D genome organization. It provides researchers with a range of functions to explore spatial genome architecture and identify regulatory elements.
dask Aces, Faster Library Computational Software Computer & Information Sciences Dask makes it easy to scale the Python libraries that you know and love like NumPy, pandas, and scikit-learn. It also allows you to Parallelize any Python code with Dask Futures, letting you scale any function and for loop, and giving you control and power in any situation.
Description Source: https://www.dask.org/
Parallel Computing, Scalability, Efficient Task Scheduling, Integration With Existing Libraries Like Numpy, Pandas, & Scikit-Learn Parallel Computing, Scalable Computing, Analytics, Data Science https://www.dask.org/ https://docs.dask.org/en/latest/api.html https://docs.dask.org/en/latest/10-minutes-to-dask.html
https://tutorial.dask.org/
https://www.youtube.com/watch?v=mqdglv9GnM8
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021.9.1, 2022.1.0, 2022.10.0
Faster: 2.8.0-Python-3.7.4, 2.18.1-Python-3.8.2, 2021.2.0, 2022.1.0, 2022.7.0, 2022.10.0
Dask is a flexible parallel computing library for analytic computing, designed to scale from single machines to large clusters. It provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
datasets Anvil Organized Collections Of Data, Structured Format For Analysis, Support For Processing & Sharing, Used To Draw Insights & Build Models Data, Research, Analysis, Processing, Sharing Anvil: https://www.rcac.purdue.edu/software/datasets Anvil: Datasets Datasets refer to collections of data that are organized and structured in a specific format for analysis, processing, and sharing. They are used in various research fields to draw insights, build models, and validate theories.
db Aces, Faster Library Database Library Computer & Information Sciences, Computer Science Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. 1. Simple and easy-to-use interface for database operations. 2. Support for common database operations like creating tables, inserting data, querying data, updating records, and deleting records. 3. Lightweight and minimalistic design for quick integration into Python projects. Database, Python Library Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 18.1.40
Faster: 18.1.32, 18.1.40
db is a simple and minimalistic database library for Python, designed to provide a lightweight interface for basic database operations.
db_file Faster Tool Database Management Computer & Information Sciences Create & Manage Database Files, Execute Queries On Database Files, Extract Data From Database Files, Modify & Update Database Files Database Management, Data Manipulation, Querying, Data Extraction Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.855, 1.856, 1.858 db_file is a software tool designed for managing and manipulating database files. It provides functionalities for creating, modifying, querying, and extracting data from database files.
dbcsr Aces, Faster Library Other Natural Sciences DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations. 1. Creation of distributed block-sparse matrix data structures
2. Efficient operations on block-sparse matrices
3. Designed for high-performance computing (HPC) applications
4. Supports parallel computation
5. Optimized for large, sparse matrices
Hpc, Sparse Matrices, Parallel Computing Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.5.0, 2.6.0
Faster: 2.5.0
dbcsr (distributed block compressed sparse row) is a library for creating distributed block-sparse matrix data structures and performing operations on them efficiently. It is designed for high-performance computing (HPC) applications that involve large, sparse matrices.
dbd-mysql Faster Software Library Database Interface Driver Computer & Information Sciences 1. Allows Perl scripts to connect to a MySQL database.
2. Provides a set of functions for database management, querying, and manipulation.
3. Supports efficient integration of MySQL database functionality within Perl applications.
Database, Mysql Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.050-Perl-5.30.0 DBD::mysql is the Perl5 Database Interface driver for the MySQL database. In other words, DBD::mysql is an interface between the Perl programming language and the MySQL programming API that comes with the MySQL relational database management system.
dbg2olc Anvil Genome Assembly Software Bioinformatics Tool Biological Sciences Genome Assembly Bioinformatics Dbg2olc is used for efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies. De Bruijn Graph Assembly, Overlap-Layout-Consensus Algorithm, Hybrid Assembly Using Long & Short Reads, Efficient Assembly Of Large & Complex Genomes Genome Assembly, De Bruijn Graph, Olc Algorithm, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/dbg2olc Anvil: 20180222, 20200723 dbg2olc is a tool developed for genome assembly using a de Bruijn graph based on overlap-layout-consensus (OLC) algorithm. It aims to efficiently assemble large and complex genomes by utilizing both long and short reads.
dbus Aces, Faster Middleware System Software Computer & Information Sciences D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
Description Source: https://www.freedesktop.org/wiki/Software/dbus/
1. Interprocess communication between applications. 2. Coordination of process lifecycle management. 3. Suitable for use in both small and large systems. 4. Enables communication between applications written in different programming languages. Message Bus System, Interprocess Communication, Process Lifecycle Management https://www.freedesktop.org/wiki/Software/dbus/ https://dbus.freedesktop.org/doc/dbus-specification.html https://dbus.freedesktop.org/doc/dbus-tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.13.18, 1.14.0, 1.15.2, 1.15.4
Faster: 1.13.12, 1.13.18, 1.14.0, 1.15.2, 1.15.4
D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle management.
dbus-glib Aces, Faster Api Library Computer & Information Sciences D-Bus is a message bus system, a simple way for applications to talk to one another. dbus-glib provides a high-level API for interacting with D-Bus, allowing applications to publish objects and call methods on remote objects over the D-Bus. D-Bus, Inter-Process Communication, Glib Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.112
Faster: 0.112
D-Bus is a message bus system for inter-application communication and coordination. dbus-glib is a library for GLib based applications to communicate with D-Bus.
dcmtk Aces, Faster Data Processing & Analysis Library & Applications Medical & Health Sciences Medical Biotechnology Medical & Health Sciences DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling storage media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers.
Description Source: https://dicom.offis.de/dcmtk/
DICOM image file examination, construction, and conversion; Handling offline media; Sending and receiving images over a network connection; Demonstrative image processing; Pattern recognition techniques. Dicom, Medical Imaging, Healthcare, Image Processing https://dicom.offis.de/dcmtk/ https://support.dcmtk.org/docs/ https://support.dcmtk.org/redmine/projects/dcmtk/wiki/Howto Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.6.7
Faster: 3.6.7
DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image processing, and pattern recognition techniques.
ddt Bridges-2, Stampede3 Debugger Development Tool Computer & Information Sciences Linaro DDT is the number one server and HPC debugger in research, industry, and academia for software engineers and scientists developing C++, C, Fortran parallel and threaded applications on CPUs, GPUs, Intel and Arm. Linaro DDT is the trusted debugging tool for ensuring program correctness for applications ranging from single process to exascale.
Description Source: https://www.linaroforge.com/linaroDdt/
DDT offers intuitive graphical user interface, multi-language support for C, C++, and Fortran, advanced debugging capabilities, memory debugging, parallel debugging for MPI, OpenMP, and hybrid codes, performance analysis for identifying bottlenecks, debugging in a distributed environment, and efficient visualization of program behavior. Debugging Tool, Performance Analysis, Parallel Computing, Serial Computing https://www.linaroforge.com/linaroDdt/ https://docs.linaroforge.com/23.1.1/html/forge/ddt/index.html https://docs.linaroforge.com/23.0.3/html/forge/worked_examples_appendix/mmult/index.html#
https://docs.linaroforge.com/23.0.3/html/forge/general_troubleshooting_appendix/index.html
Bridges-2: https://www.psc.edu/resources/software/ddt
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Bridges-2: 20.1.3, 20.2.1, 23.0.3
Stampede-3: 23.1.2
DDT is a powerful, flexible, scalable, and easy-to-use debugging and performance analysis tool for parallel and serial codes.
dealii Bridges-2 Library deal.II — a name that originally meant to indicate that it is the successor to the Differential Equations Analysis Library — is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. It uses state-of-the-art programming techniques to offer you a modern interface to the complex data structures and algorithms required.
Description Source: https://www.dealii.org/about.html
https://www.dealii.org/ https://www.dealii.org/current/doxygen/deal.II/index.html https://www.dealii.org/developer/doxygen/deal.II/step_1.html
https://www.dealii.org/developer/doxygen/deal.II/step_2.html
Bridges-2: https://www.psc.edu/resources/software/dealii Bridges-2: 9.2.0, 9.3.1
Stampede-3: 9.5.2
debreak Anvil Bioinformatics Tool Analysis Tool Biological Sciences Debreak is a SV caller for long-read single-molecular sequencing data. decons debreak allows users to easily interpret the results of debarcoder by providing visualization and statistical analysis tools. It helps in understanding the performance of the CRISPR screen and identifying significant hits. Bioinformatics, Hpc Tools Anvil: https://www.rcac.purdue.edu/software/debreak Anvil: 1.3 debreak is a tool for analyzing and visualizing the output generated by the debarcoder software. Debarcoder is used for decoding high-throughput sequencing data from combinatorial CRISPR screens.
debugger Kyric Debugger Development Tools Engineering & Technology Stepping Through Code, Inspecting Variables, Setting Breakpoints, Analyzing Program Execution Flow Debugging, Software Development Kyric: Latest, 10.0.0 A debugger is a software tool that allows programmers to track down and fix bugs (errors) in their programs. It enables users to step through code, inspect variables, set breakpoints, and analyze the program's execution flow.
decona Faster Conda Package Manager Package Management Tool Other Computer & Information Sciences Decona provides a user-friendly interface for creating, managing, and sharing Conda environments. It enables users to easily install, update, and remove Conda packages, as well as manage dependencies and virtual environments. Conda, Package Management, Software Installation, Dependency Management Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.1.2-Python-3.7.4 Decona is a Conda package management tool that simplifies the installation and management of software packages, dependencies, and environments through the Conda package manager.
deconseq Anvil Analysis Tool Bioinformatics Tool Biological Sciences DeconSeq: DECONtamination of SEQuence data using a modified version of BWA-SW. 1. Removal of contaminating sequences from datasets
2. Detection of contamination based on user-defined criteria
3. Support for various sequence formats
4. Customizable parameters for tailored analysis
5. Efficient processing of high-throughput sequencing data
Bioinformatics, Sequence Analysis, Metagenomics Anvil: https://www.rcac.purdue.edu/software/deconseq Anvil: 0.4.3 DeconSeq is a novel program specifically designed to automatically decontaminate sequences and detect possible contamination in sequence datasets. It efficiently detects and removes sequence contamination from high-throughput sequencing reads. The tool is particularly useful in metagenomics studies to ensure the quality and accuracy of the analysis results.
deepbgc Anvil Bioinformatics Tool Computational Tool Biological Sciences Bioinformatics Biological Sciences Deepbgc is a tool for BGC detection and classification using deep learning. 1. Detection of biosynthetic gene clusters (BGCs) in microbial genomes. 2. Classification of BGCs based on the type of specialized metabolites they produce. 3. Utilizes deep learning algorithms for improved accuracy in BGC prediction. 4. Allows for the exploration and visualization of identified BGCs. Biosynthetic Gene Clusters, Microbial Genomes, Deep Learning, Metabolites Anvil: https://www.rcac.purdue.edu/software/deepbgc Anvil: 0.1.26, 0.1.30 DeepBGC is a tool for the detection and classification of biosynthetic gene clusters in microbial genomes using deep learning techniques. It focuses on identifying gene clusters responsible for the production of specialized metabolites.
deepconsensus Anvil Tool Bioinformatics Biological Sciences DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data. 1. Variant calling in MinION nanopore sequencing data
2. Utilizes deep learning for improved accuracy and sensitivity
3. Detection of single nucleotide variants (SNVs) and insertion/deletion (indel) mutations
Variant Calling, Minion Nanopore Sequencing, Deep Learning Anvil: https://www.rcac.purdue.edu/software/deepconsensus Anvil: 0.2.0 DeepConsensus is a tool for variant calling in MinION nanopore sequencing data. It uses deep learning to increase accuracy and sensitivity in detecting single nucleotide variants (SNVs) and insertion/deletion (indel) mutations.
deepdiff Aces Python Library Library Computer & Information Sciences DeepDiff is a Python library that provides comprehensive and detailed diffing capabilities, allowing for the deep comparison of data structures within Python. It is capable of identifying differences between dictionaries, lists, sets, and other complex data types, making it highly useful for tasks that require detailed tracking of changes or discrepancies in data over time, such as data analysis, testing, and debugging. 1. Deep comparison of dictionaries, lists, sets, and strings
2. Visualization of the differences between two objects
3. Ability to ignore specific keys or paths during comparison
4. Customizable comparison options and formatting
Python Library, Data Comparison, Object Comparison https://github.com/seperman/deepdiff https://zepworks.com/deepdiff/current/diff.html https://zepworks.com/posts/deepdiff-tutorial-compare-numbers/ Aces: https://hprc.tamu.edu/software/aces/ Aces: 5.8.1, 6.7.1 DeepDiff is a Python library for deep (nested) comparisons of objects.
deepsignal2 Anvil Toolkit Bioinformatics Biological Sciences Genomics Genetics Deepsignal2 is a deep-learning method for detecting DNA methylation state from Oxford Nanopore sequencing reads. 1. Process raw nanopore signal data
2. Detect DNA modifications and structural variations
3. Utilizes deep learning algorithms for improved accuracy
4. Supports real-time analysis of nanopore sequencing data
Nanopore Sequencing, Deep Learning, Signal Processing, Variant Detection Anvil: https://www.rcac.purdue.edu/software/deepsignal2 Anvil: 0.1.2 Deepsignal2 is a deep learning-based toolkit for nanopore signal processing and variant detection. It is designed to accurately detect DNA modifications and structural variants from raw nanopore sequencing data.
deeptools Anvil Analysis Tool Bioinformatics Biological Sciences Genomics Biology deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
Description Source: https://deeptools.readthedocs.io/en/latest/
Quality Control Of Sequencing Data, Normalization Of Chip-Seq & Atac-Seq Data, Visualization Of Genomic Data, Statistical Analysis Of High-Throughput Sequencing Data Bioinformatics, Hpc Tools, Computational Software https://github.com/deeptools/deepTools https://deeptools.readthedocs.io/en/latest/content/api.html https://deeptools.readthedocs.io/en/latest/content/list_of_tools.html
https://deeptools.readthedocs.io/en/develop/content/example_usage.html
Anvil: https://www.rcac.purdue.edu/software/deeptools Anvil: 3.5.1-Py DeepTools is a suite of tools for the analysis of high-throughput sequencing data, with a focus on ChIP-seq and ATAC-seq data. It provides various functions for quality control, normalization, visualization, and downstream analysis of sequencing data.
deepvariant Anvil Variant Caller Genomics Biological Sciences Bioinformatics Genomics DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. 1. Utilizes deep neural networks for variant calling
2. Provides accurate and reliable variant identification
3. Supports germline and somatic variant calling
4. Optimized for identifying small variants like single nucleotide polymorphisms (SNPs) and insertions/deletions (indels)
5. Employs a peer-reviewed, open-source methodology for variant calling
Variant Calling, Genetic Variants, Deep Learning, DNA Sequencing Anvil: https://www.rcac.purdue.edu/software/deepvariant Anvil: 1.0.0, 1.1.0 DeepVariant is a deep learning-based variant caller developed by Google Brain that accurately identifies genetic variants from next-generation DNA sequencing data.
default Delta Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: Default
default-environment Expanse Default Environment Environment Setup Loads default environment modules for this cluster Includes Popular Programming Languages Such As Python, C++, Java, & Others, Common Utilities Like Text Editors, Version Control Systems, & Package Managers Are Pre-Installed, Support For Compiling Code, Managing Dependencies, & Running Basic Scripts, Can Be Easily Extended & Customized With Additional Software Packages & Libraries Development-Environment, Computational-Tools, Software-Utilities Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Default-Environment The default-environment is a basic system setup that provides essential tools and configurations for software development and computational work. It serves as a starting point for creating custom environments tailored to specific requirements and preferences.
default-s11 Delta Bioinformatics Tool Computational Software Biological Sciences Bioinformatics Biological Sciences The software offers advanced tools for sequence alignment, protein structure prediction, molecular docking, and molecular dynamics simulations. It provides multiple algorithms for analyzing biological sequences and predicting protein structures. Default-S11 also includes visualization capabilities for molecular dynamics simulations. Computational Software, Bioinformatics, Molecular Dynamics, Sequence Analysis, Protein Structure Prediction Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: Default-S11 Default-S11 is a high-performance computational software designed for bioinformatics analysis and molecular dynamics simulations.
defaultmodules Expanse Libraries/Modules Development Tools Other Not Applicable Not Applicable Predefined Software Packages Or Libraries Included With Software Installations, Essential Tools For Various Tasks Within The Software Ecosystem Software Libraries, Software Packages, Default Modules Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Defaultmodules Default modules are predefined software packages or libraries that are included with the installation of a particular software, compiler, or programming environment. These modules typically consist of commonly used tools or libraries that are essential for various tasks within the software ecosystem.
delly Anvil Tool Bioinformatics Biological Sciences Structural Variant Discovery Genomics Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. 1. Integrates multiple SV detection methods
2. Identifies deletions, inversions, duplications, and translocations
3. Provides high accuracy in SV discovery
4. Offers visualization tools for easy interpretation of results
Structural Variant Discovery, Sv Detection, Genomics Anvil: https://www.rcac.purdue.edu/software/delly Anvil: 0.9.1, 1.0.3, 1.1.3, 1.1.5, 1.1.6 Delly is a structural variant discovery tool that integrates multiple SV detection methods to accurately identify deletions, inversions, duplications, and translocations.
dendropy Anvil, Faster Computational Library Biological Sciences Evolutionary Biology Biological Sciences DendroPy is a Python library for phylogenetic computing. Read & Write Phylogenetic Tree Files In Various Formats, Perform Tree Manipulations, Transformations, & Calculations, Simulate Trees Under A Variety Of Models & Conditions, Analyze & Visualize Phylogenetic Data, Supports A Wide Range Of Phylogenetic Analysis Tools & Methods Phylogenetics, Computational Biology, Python Library, Bioinformatics, Phylogenetic Trees Anvil: https://www.rcac.purdue.edu/software/dendropy
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 4.5.2
Faster: 4.5.2
DendroPy is a flexible and modular phylogenetic computing library in Python, offering reading, writing, simulation, and manipulation of phylogenetic trees and associated data.
desmond Bridges-2, Faster Molecular Dynamics Software Simulation Software Biological Sciences Structural Biology Biochemistry & Molecular Biology Molecular Dynamics Simulations, Protein-Ligand Interactions, Free Energy Calculations, Structural Refinement Molecular Dynamics, Biological Systems, Drug Discovery, Protein Folding Bridges-2: https://www.psc.edu/resources/software/desmond
Faster: https://hprc.tamu.edu/software/faster/
Bridges-2: 2020.4
Faster: 2020-1, 2021-1
Desmond is a molecular dynamics simulation software designed for studying biological systems at the atomic level. It is widely used for drug discovery, protein folding, and molecular interactions.
dev-utilities Kyric Tools Development Tools Computer & Information Sciences, Other Computer & Information Sciences Code editors, version control systems, build automation tools, testing frameworks, debugging tools, package managers, linters, code formatters, code generators, documentation generators, continuous integration/delivery tools. Development, Utilities Kyric: Latest, 2021.1.1 Dev-utilities is a collection of various development utilities that assist software developers in various aspects of the development process. These utilities can range from code editors and version control systems to build automation tools and testing frameworks.
devito Faster Compiler Computational Science, Optimization Applied Mathematics Seismic Imaging, Inverse Problems Numerical Analysis High-Level Symbolic Problem Definition, Automatic Optimization Of Finite Difference Kernels, Geared Towards Seismic Imaging & Inversion, Supports A Range Of Pde Problems Finite Difference Compiler, Pde Solver, Computational Science Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.6.1-Python-3.8.2 Devito is a high-level finite difference compiler for solving partial differential equations (PDEs). It generates and optimizes finite difference kernels to achieve high performance on modern computer architectures.
dft-d3 Faster Library Computational Software Chemical Sciences Chemical Sciences Physical Sciences 1. Dispersion correction method for DFT calculations.
2. Accounts for long-range dispersive interactions.
3. Improves description of non-bonded interactions and van der Waals forces.
4. Enhances the accuracy of DFT calculations in molecular systems.
Computational Chemistry, Density Functional Theory, Quantum Mechanics Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.2.0 DFT-D3 is a widely used dispersion correction method for density functional theory (DFT) calculations to accurately account for long-range dispersive interactions in molecular systems. It improves the description of non-bonded interactions, including van der Waals forces, and enhances the accuracy of DFT calculations.
dftbplus Expanse DFTB+ is an implementation of the Density Functional based Tight Binding (DFTB) method, containing many extensions to the original method. Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 19.1-Openblas
diamond Anvil, Expanse, Faster Bioinformatics Tool Sequence Aligner Biological Sciences Genomics, Proteomics Bioinformatics Diamond is sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. High-Performance Sequence Aligner For Protein & Translated DNA Searches, Optimized For Aligning Data From Ngs Machines, Utilizes The Diamond Heuristic Aligner For Rapid Alignment, Supports Sensitive Alignment Of Multiple Query Sequences Against A Large Sequence Database, Provides Significant Speedup Compared To Blast Tools Sequence Alignment, Ngs Analysis, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/diamond
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.0.13, 2.0.14, 2.0.15, 2.1.6
Expanse: 0.9.25
Faster: 2.0.13, 2.1.0
Diamond is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of protein sequence data utilizing the Diamond heuristic aligner. It is particularly optimized for aligning sequencing reads produced by next-generation sequencing (NGS) machines.
diffutils Kyric Text Processing Utility Engineering & Technology 1. Generating line-by-line differences between text files.
2. Showing changes between files in a user-friendly format.
3. Comparing files at byte level with detailed output.
4. Merging changes from multiple versions of a file.
Text Comparison, File Difference, Text Analysis, Version Control https://www.gnu.org/software/diffutils/ https://www.gnu.org/software/diffutils/manual/diffutils.html https://www.gnu.org/software/diffutils/manual/html_node/Invoking-diff.html#Invoking-diff Diffutils is a collection of utilities for comparing and finding differences between text files. It includes programs like `diff` for showing the differences between two files, `cmp` for comparing two files byte by byte, and `diff3` for comparing three files.
dill Aces, Faster Library Serialization Library Computer & Information Sciences dill extends Python’s pickle module for serializing and de-serializing Python objects to the majority of the built-in Python types.
Description Source: https://dill.readthedocs.io/en/latest/
1. Supports the serialization of almost all Python data types.
2. Can serialize functions and classes.
3. Supports lambda functions.
4. Provides a mechanism to serialize instances of un-picklable classes.
5. Allows for easy storage and retrieval of Python objects.
Serialization, Python, Datastructures, Library https://pypi.org/project/dill/ https://dill.readthedocs.io/en/latest/ https://dill.readthedocs.io/en/latest/#basic-usage
https://github.com/uqfoundation/dill?tab=readme-ov-file#more-information
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.3.4, 0.3.6, 0.3.7
Faster: 0.3.4, 0.3.6, 0.3.7
Dill is a serialization library for Python datastructures. It provides the ability to serialize all standard Python data types without needing to be pre-informed about their existence, offering extended functionality beyond what is available in the standard `pickle` library.
dimemas Kyric Performance Prediction Tool Simulation Tool Engineering & Technology Automatic Performance Prediction, Simulation Techniques, Estimation Of Parallel Application Performance On Large-Scale Systems Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems https://tools.bsc.es/dimemas https://github.com/bsc-performance-tools/dimemas/blob/master/cfgs/ideal.cfg https://tools.bsc.es/doc/introduction_dimemas.pdf
https://tools.bsc.es/sites/default/files/documentation/slides/Dimemas-Hands-On.pdf
Kyric: 5.4.2 DIMemas is a software tool for the automatic performance prediction of parallel applications. It utilizes simulation techniques to estimate the performance of parallel applications on large-scale systems.
dlib Faster Library Toolkit Computer & Information Sciences Machine Learning Algorithms, Computer Vision, Face Detection, Object Detection, Facial Landmarks, Pose Estimation Machine Learning, Computer Vision, Object Detection, Facial Recognition, Pose Estimation Faster: https://hprc.tamu.edu/software/faster/ Faster: 19.22-Cuda-11.3.1 dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems. It is used in a wide range of applications including computer vision, face detection, object detection, facial landmarks, pose estimation, and more.
dm-reverb Faster Python Library Library Computer Science Efficient Data Loading & Storage, Designed For Deep Learning & Machine Learning Projects, Flexible Api, Supports Storing Data On Disk, Suitable For Use With Tensorflow Python Library, Data Loading, Data Storage, Machine Learning, Deep Learning Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.2.0 dm-reverb is a Python library for efficient data loading and storage in deep learning and machine learning projects, particularly designed for use with TensorFlow. It provides a simple and flexible API for managing large datasets by storing data on disk and loading it into memory in a suitable format for training models.
dm-tree Aces, Faster Library Scientific Computing Computer & Information Sciences dm-tree is a python library for working with nested data structures. In a way, tree generalizes the builtin map function which only supports flat sequences, and allows to apply a function to each "leaf" preserving the overall structure.
Description Source: https://github.com/google-deepmind/tree
Efficient Manipulation Of Tree Structures, Support For Nested & Hierarchical Data, Traversal & Querying Capabilities, Serialization & Deserialization Of Tree Data Python Library, Hierarchical Data, Tree Structures, Data Manipulation https://github.com/google-deepmind/tree https://tree.readthedocs.io/en/latest/api.html https://tree.readthedocs.io/en/latest/recipes.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.1.6, 0.1.8
Faster: 0.1.5, 0.1.6, 0.1.8
dm-tree is a Python library for manipulating nested tree-like data structures with ease and efficiency. It provides a comprehensive set of tools for working with hierarchical data in a user-friendly manner.
dnaapler Anvil Prediction Tool Bioinformatics Tool Biological Sciences Bioinformatics Genomics dnaapler is a simple python program that takes a single nucleotide input sequence (in FASTA format), finds the desired start gene using blastx against an amino acid sequence database, checks that the start codon of this gene is found, and if so, then reorients the chromosome to begin with this gene on the forward strand. 1. Prediction of DNA replication origins
2. Machine learning-based approach
3. Identification of replication initiation sites in microbial genomes
Bioinformatics, Tool, DNA Replication, Genomics Anvil: https://www.rcac.purdue.edu/software/dnaapler Anvil: 0.1.0 dnaapler is a bioinformatics tool for predicting DNA replication origins in microbial genomes. It uses machine learning models trained on replication initiation sites to identify potential origins of replication.
dnaio Anvil Python Library Library Biological Sciences Genetics Bioinformatics Dnaio is a Python 3.7+ library for very efficient parsing and writing of FASTQ and also FASTA files. Efficient Reading & Writing Of DNA Sequences, Compatibility With Various Sequence File Formats, Optimized For High Performance, Integration With Bioinformatics Pipelines Python Library, Bioinformatics, DNA Sequences, Sequence Data Anvil: https://www.rcac.purdue.edu/software/dnaio Anvil: 0.8.1 dnaio is a Python library for reading and writing DNA sequences efficiently. It provides high-performance I/O operations for DNA sequence data, allowing for seamless integration into bioinformatics workflows.
dnnl Kyric Deep Learning Library Library Computer & Information Sciences Deep Learning Artificial Intelligence & Intelligent Systems 1. Efficient deep learning neural network layer implementations. 2. Open-source and highly optimized for performance. 3. Support for various hardware platforms. 4. Integration with popular deep learning frameworks like TensorFlow and PyTorch. Deep Learning, Neural Networks, Machine Learning, Performance Optimization https://github.com/oneapi-src/oneDNN https://oneapi-src.github.io/oneDNN/ https://oneapi-src.github.io/oneDNN/dev_guide_examples.html Kyric: Latest, 2021.1.1 Deep Neural Network Library (DNNL) is an open-source, performance-oriented library for deep learning applications. Formerly known as Intel Math Kernel Library for Deep Neural Networks (MKL-DNN), it provides optimized building blocks for implementation of deep learning neural network layers on various hardware platforms.
dnnl-cpu-gomp Kyric Computational Software Libraries & Frameworks Computer & Information Sciences Optimized For Deep Neural Network Computations On Cpus, Utilizes Openmp For Parallelism In Thread Processing, Includes Various Functions & Operations For Neural Network Implementations, Supports Efficient Execution Of Deep Learning Models On Cpu Architectures Deep Learning, Neural Networks, Openmp, Cpu Computing https://github.com/oneapi-src/oneDNN https://oneapi-src.github.io/oneDNN/ https://oneapi-src.github.io/oneDNN/dev_guide_examples.html Kyric: Latest, 2021.1.1 The dnnl-cpu-gomp is an open-source deep neural network library developed for CPU-based computations employing OpenMP (Open Multi-Processing) as a thread-processing technology.
dnnl-cpu-iomp Kyric Intel Ai/Ml Computer & Information Sciences 1. Accelerates deep learning inferencing on CPU.
2. Utilizes Intel OpenMP for parallel processing.
3. Optimized for performance with deep neural network computations on Intel CPUs.
Deep Learning, Optimization, Cpu Acceleration https://github.com/oneapi-src/oneDNN https://oneapi-src.github.io/oneDNN/ https://oneapi-src.github.io/oneDNN/dev_guide_examples.html Kyric: Latest, 2021.1.1 dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance.
dnnl-cpu-tbb Kyric Intel Ai/Ml https://github.com/oneapi-src/oneDNN https://oneapi-src.github.io/oneDNN/ https://oneapi-src.github.io/oneDNN/dev_guide_examples.html Kyric: Latest, 2021.1.1
docker Expanse Virtualization Containerization Platform Computer & Information Sciences Containerization Of Applications, Efficient & Lightweight, Portability Across Environments, Automated Deployment, Scalability, Isolation Of Applications Containerization, Deployment, Scalability, Isolation Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 20.10.21 Docker is a platform that enables users to develop, ship, and run applications within containers. Containers allow developers to package up an application with all parts it needs, such as libraries and other dependencies, and ship it all out as one package.
docker-user Aces Rootless mode allows running the Docker daemon and containers as a non-root user to mitigate potential vulnerabilities in the daemon and the container runtime. Rootless mode executes the Docker daemon and containers inside a user namespace. To start the daemon: 'dockerd-rootless-setuptool.sh install --skip-iptables'. To test it: 'docker run hello-world'. To stop the daemon: 'dockerd-rootless-setuptool.sh uninstall --skip-iptables' Aces: https://hprc.tamu.edu/software/aces/ Aces: 202311
dorado Aces Tool Software Engineering & Technology Sciences Biology Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
Description Source: https://github.com/nanoporetech/dorado
Dorado provides capabilities for analyzing parallel application performance, identifying bottlenecks, measuring scalability, and optimizing code efficiency. It offers detailed performance metrics and visualizations to help users understand the behavior of their applications on parallel architectures. Performance Evaluation, Benchmarking, Hpc, Supercomputing https://github.com/nanoporetech/dorado https://dorado.readthedocs.io/en/latest/dorado/index.html#reference-api https://dorado.readthedocs.io/en/latest/dorado/index.html#getting-started-with-dorado
https://dorado.readthedocs.io/en/latest/dorado/core.html
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.5.2-Cuda-11.8.0
Bridges-2: 0.6.0
Dorado is a software tool used for performance evaluation and benchmarking in HPC (High-Performance Computing) environments. It allows users to assess the performance of parallel applications and optimize their running times on supercomputers and clusters.
dos2unix Delta Utility Data Management Computer & Information Sciences dos2unix converts text files with DOS or Mac line breaks to Unix line breaks and vice versa.
Description Source: https://dos2unix.sourceforge.io/#DOS2UNIX
1. Converts text files from DOS/Windows line endings (CRLF) to Unix line endings (LF).
2. Preserves the file ownership, permissions, and timestamps.
3. Can handle conversion of multiple files in batch mode.
Text Conversion, Line Endings, Command-Line Utility https://waterlan.home.xs4all.nl/dos2unix.html https://waterlan.home.xs4all.nl/dos2unix/man1/dos2unix.htm https://waterlan.home.xs4all.nl/dos2unix/man1/dos2unix.htm#EXAMPLES Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 7.4.4 dos2unix is a command-line utility that converts text files with DOS or Windows line endings (CRLF) to Unix line endings (LF) format.
dot Ookami Graph Visualization Software Visualization Tool Computer & Information Sciences Graph layout programs, web and interactive graphical interfaces, auxiliary tools, libraries, language bindings Graph Visualization, Open Source, Graph Layout Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: Dot Graphviz is open source graph visualization software. It has several main graph layout programs. It also has web and interactive graphical interfaces, and auxiliary tools, libraries, and language bindings.
double-conversion Aces, Faster Library Computer & Information Sciences Double-Conversion provides binary-decimal and decimal-binary routines for IEEE doubles. This library consists of efficient conversion routines that have been extracted from the V8 JavaScript engine.
Description Source: https://github.com/google/double-conversion
1. Efficient conversion of double-precision floating-point numbers.
2. High precision in decimal string conversion.
3. Optimized for performance.
4. Supports both converting double to string and parsing strings into doubles.
Conversion, Performance, Precision https://github.com/google/double-conversion https://github.com/google/double-conversion/blob/master/double-conversion/string-to-double.h https://github.com/google/double-conversion/blob/master/test/cctest/test-conversions.cc Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.1.5, 3.2.0, 3.2.1, 3.3.0
Faster: 3.1.4, 3.1.5, 3.2.0, 3.2.1, 3.3.0
double-conversion is a performant library for converting double-precision floating-point values to and from decimal strings, designed for high-performance and precision in conversions.
doxygen Aces, Expanse, Faster, Ookami Tool Documentation Generation Software Engineering, Systems, & Development Doxygen is a widely-used documentation generator tool in software development. It automates the generation of documentation from source code comments, parsing information about classes, functions, and variables to produce output in formats like HTML and PDF.
Description Source: https://www.doxygen.nl/
Automatic Generation Of Documentation From Source Code, Support For Multiple Programming Languages Including C++, Objective-C, C#, Java, Python, Etc., Output Documentation In Various Formats Such As Html, Latex, Rtf, Xml, & Man Pages, Support For Code Cross-Referencing, Inheritance Diagrams, Collaboration Diagrams, & More Documentation Generator, Software Development, Programming https://www.doxygen.nl/ https://www.doxygen.nl/manual/index.html https://www.doxygen.nl/manual/starting.html
https://www.doxygen.nl/manual/doxygen_usage.html
https://www.youtube.com/watch?v=LZ5E4vEhsKs
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 1.8.20, 1.9.1, 1.9.4, 1.9.5, 1.9.7, 1.9.8
Expanse: 1.8.17
Faster: 1.8.14, 1.8.16, 1.8.17, 1.8.20, 1.9.1, 1.9.4, 1.9.5, 1.9.7, 1.9.8
Ookami: 1.9.5
Doxygen is a documentation generator tool that is used to generate software reference documentation from annotated source code. It supports multiple programming languages and produces output in various formats, including HTML, LaTeX, RTF, and more.
dpct Kyric Development Compiler Compiler Computer & Information Sciences Supports C++ programming model for NVIDIA GPUs, enables users to write C++ code for parallel execution on GPUs, allows compilation of C++ code to target CUDA architecture, provides accelerated computing capabilities. Cuda Programming, Gpu Computing, Parallel Programming https://github.com/ilastik/dpct/ https://github.com/ilastik/dpct/blob/main/README.md https://github.com/ilastik/dpct/blob/main/test/test.py Kyric: Latest, 2021.1.1 Data Parallel C++ for CUDA is a C++ programming model for accelerators based on the NVIDIA CUDA architecture. It allows users to write C++ code that can be compiled to target NVIDIA GPUs using CUDA for parallel execution.
dpl Kyric It provides tools for analyzing the structure and syntax of programming languages directly. Programming Language Analysis, Syntax Analysis, Language Structure Analysis https://github.com/travis-ci/dpl https://www.rubydoc.info/github/travis-ci/dpl https://www.rubydoc.info/github/travis-ci/dpl/Dpl/Examples#cmds-instance_method Kyric: Latest, 2021.1.1 dpl is a software for performing direct programming language analysis.
draco Aces, Faster Library Computer & Information Sciences Draco is a library for compressing and decompressing 3D geometric meshes and point clouds. It is intended to improve the storage and transmission of 3D graphics. 1. High compression ratios for 3D geometric data
2. Maintains geometric integrity during compression and decompression
3. Supports both mesh and point cloud data formats
4. Optimized for performance and memory usage
5. Portable and easy to integrate into existing software pipelines
Compression, 3D Graphics, Geometric Data, Mesh, Point Cloud Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.5.6
Faster: 1.5.6
Draco is a software library for compressing and decompressing 3D geometric meshes and point clouds. It is designed to improve the storage and transmission of 3D graphics data by offering high compression ratios while maintaining the geometric integrity of the data.
dragonflye Anvil Computational Software Analysis & Visualization Tools Biological Sciences Systems Biology Bioinformatics Dragonflye is a pipeline that aims to make assembling Oxford Nanopore reads quick and easy. drep: drep/3.2 Some of the core features of Dragonflye include network visualization, pathway analysis, gene expression data integration, network clustering, and network motif identification. It allows users to explore and analyze large-scale biological networks to identify key regulatory elements and functional modules. Biology, Network Analysis, Pathway Analysis Anvil: https://www.rcac.purdue.edu/software/dragonflye Anvil: 1.0.13, 1.0.14 Dragonflye is a computational software package designed for the analysis and visualization of biological networks and pathways. It offers tools for studying the interactions between genes, proteins, and other biological molecules to gain insights into complex biological processes.
drep Anvil Bioinformatics Algorithm/Tool Biological Sciences Drep is a python program for rapidly comparing large numbers of genomes. Dereplication Of Microbial Genomes, Identification & Removal Of Duplicate Sequences, Improving Efficiency & Accuracy Of Downstream Analyses Microbiome, Genome Analysis, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/drep Anvil: 3.2.2 drep (Dereplicator) is a tool for fast and accurate dereplication of genomes in microbial datasets. It helps to identify and remove duplicate sequences to ensure that downstream analyses are not biased by redundant data.
drop-seq Anvil Bioinformatics Computational Tool Biological Sciences Genetics Biological Sciences Drop-seq are java tools for analyzing Drop-seq data. 1. Enables analysis of gene expression profiles at the single-cell level
2. Utilizes microfluidic techniques for high-throughput single-cell RNA sequencing
3. Allows for the identification of cell types and characterization of cell populations within heterogeneous samples
4. Provides a platform for studying gene expression dynamics in individual cells
5. Facilitates the discovery of rare cell types and transitional cell states
Single-Cell RNA Sequencing, Gene Expression Analysis, Microfluidics, Cellular Heterogeneity, Transcriptomics Anvil: https://www.rcac.purdue.edu/software/drop-seq Anvil: 2.5.2 Drop-seq is a computational method that enables biologists to analyze the gene expression profiles of thousands of individual cells in a single experiment. It is designed to perform single-cell RNA sequencing using microfluidic techniques.
dropest Anvil Tool Statistical Software Statistics & Probability Dropest is a pipeline for initial analysis of droplet-based single-cell RNA-seq data. Some core features of dropest include robust power calculations, sample size calculations, adjustment for non-normality in data, and computation of power curves. Statistical Software, Power Calculations, Sample Size Calculations Anvil: https://www.rcac.purdue.edu/software/dropest Anvil: 0.8.6 dropest is a statistical software package for carrying out robust power and sample size calculations in two-sample comparisons.
dsmml Delta Deep Learning Library Molecular Machine Learning Library Other Chemical Sciences Physical Chemistry Chemical Sciences The core features of dsmml include support for deep learning models such as convolutional neural networks (CNNs) and recurrent neural networks (RNNs) for molecular structure analysis, molecular property prediction, ligand-protein interaction analysis, and virtual screening. It also provides pre-trained models, dataset management tools, and visualization capabilities for interpreting model results. Deep Learning, Molecular Machine Learning, Computational Chemistry, Drug Discovery Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html dsmml is a deep learning library specifically designed for molecular machine learning applications. It offers a range of tools and techniques tailored for computational chemistry and drug discovery tasks.
dsuite Anvil Python Library Data Analysis Tool Statistics & Probability Longitudinal Data Analysis, Survival Analysis Biostatistics Dsuite provides a fast calculation of Patterson's D (ABBA-BABA) and the f4-ratio statistics across many populations/species.
Description Source: https://github.com/millanek/Dsuite
Some of the core features of dsuite include data preprocessing, model estimation for longitudinal and survival analysis, visualization tools for exploring and interpreting results, and integration with other Python libraries for statistical analysis and data visualization. Python Library, Data Analysis, Data Visualization https://github.com/millanek/Dsuite https://github.com/millanek/Dsuite?tab=readme-ov-file#commands-v05-r53 https://github.com/millanek/tutorials/tree/master/analysis_of_introgression_with_snp_data Anvil: https://www.rcac.purdue.edu/software/dsuite Anvil: 0.4.R43, 0.5.R44 Dsuite is a Python package for processing, analyzing, and visualizing longitudinal and survival data in a user-friendly way. It is designed to facilitate data exploration, estimation of parametric and non-parametric models, and visualization of results for longitudinal and survival data analysis.
dualsphysics Faster Computational Simulation Software Physical Sciences Computational Fluid Dynamics Fluid Dynamics Smoothed Particle Hydrodynamics (Sph) Simulations, Simulation Of Free-Surface Flows, Fluid-Structure Interactions Modeling, Parallel Computing Capabilities, Open-Source & Customizable, User-Friendly Interface Computational Fluid Dynamics, Fluid Dynamics, Open-Source Software, Parallel Computing, Sph Method Faster: https://hprc.tamu.edu/software/faster/ Faster: 5.0.175-Cuda-11.4.1 DualSPHysics is a popular open-source computational fluid dynamics software package based on the Smoothed Particle Hydrodynamics (SPH) method. It allows for the simulation of free-surface flows, fluid-structure interactions, and complex fluid dynamics phenomena.
dyninst Delta Tool Instrumentation & Analysis Computer & Information Sciences 1. Binary instrumentation for code analysis and modification.
2. Dynamic analysis of program behavior.
3. Program monitoring during runtime.
4. Support for C, C++, and Fortran applications.
5. Versatile and flexible for various use cases.
Binary Instrumentation, Code Analysis, Runtime Monitoring Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Dyninst is a versatile and powerful binary instrumentation and analysis tool that provides capabilities for runtime code analysis, modification, and monitoring in C, C++, and Fortran applications.
easybuild Aces, Faster, Kyric Build Automation Developer Tools Engineering & Technology EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way.
Description Source: https://docs.easybuild.io/what-is-easybuild/
Automates The Building & Installation Of Software Packages, Supports A Wide Range Of Software Packages & Libraries, Provides Easy-To-Use Configuration Options, Designed For Hpc Systems Software Building, High-Performance Computing, Automation https://easybuild.io/ https://easybuild.readthedocs.io/en/latest/ https://tutorial.easybuild.io/
https://docs.easybuild.io/using-easybuild/#specifying_easyconfigs
https://docs.easybuild.io/typical-workflow-example/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.7.1, 4.8.0, 4.8.2, 4.9.0
Faster: 4.5.1, 4.5.4, 4.5.5, 4.6.0, 4.6.2, 4.7.0, 4.7.1, 4.7.2, 4.8.2
Kyric: 4.3.0
EasyBuild is an open-source framework for building and installing software packages on High-Performance Computing (HPC) systems. It aims to make building software easier for system administrators and users on HPC systems by automating the build process.
easybuild-aces Aces Tools Software Engineering & Development Computer & Information Sciences Software Engineering, Systems, & Development Computer & Information Sciences EasyBuild environment variables for building system software in /tmp and installing in /sw/eb on aces.hprc.tamu.edu
Description Source: https://hprc.tamu.edu/software/aces/#
EasyBuild-ACES provides recipes for building software packages often used by the CCDC-ARL CISD ACES research group, allowing for easy deployment and management of these tools. Software Development, Tools, Packages https://easybuild.io/ https://easybuild.readthedocs.io/en/latest/ https://tutorial.easybuild.io/
https://docs.easybuild.io/using-easybuild/#specifying_easyconfigs
https://docs.easybuild.io/typical-workflow-example/
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0 EasyBuild-ACES is a collection of EasyBuild framework recipes for building commonly used software packages within the Army Combat Capabilities Development Command Army Research Laboratory (CCDC-ARL) Computational and Information Sciences Directorate (CISD) Advanced Computing, Engineering and Software (ACES) research group.
easybuild-aces-myeb Aces Software Repo User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb.
Description Source: https://hprc.tamu.edu/software/aces/#
https://easybuild.io/ https://easybuild.readthedocs.io/en/latest/ https://tutorial.easybuild.io/
https://docs.easybuild.io/using-easybuild/#specifying_easyconfigs
https://docs.easybuild.io/typical-workflow-example/
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0
easybuild-aces-scratch Aces Software Repo User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb.
Description Source: https://hprc.tamu.edu/software/aces/#
https://easybuild.io/ https://easybuild.readthedocs.io/en/latest/ https://tutorial.easybuild.io/
https://docs.easybuild.io/using-easybuild/#specifying_easyconfigs
https://docs.easybuild.io/typical-workflow-example/
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0
easybuild-aces-tmp Aces Tool Utilities Engineering & Technology Science & Engineering Education Infrastructure & Instrumentation EasyBuild environment variables for building in /tmp and installing in /sw/eb on aces.hprc.tamu.edu.
Description Source: https://hprc.tamu.edu/software/aces/#
1. Manages temporary directories for the EasyBuild software build and installation framework.
2. Helps in organizing and cleaning up temporary build directories for optimized performance.
3. Streamlines the build process by efficiently managing temporary storage.
Software Build, Installation Framework, Hpc Systems, Temporary Directory Management https://easybuild.io/ https://easybuild.readthedocs.io/en/latest/ https://tutorial.easybuild.io/
https://docs.easybuild.io/using-easybuild/#specifying_easyconfigs
https://docs.easybuild.io/typical-workflow-example/
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0 EasyBuild is a software build and installation framework for high-performance computing (HPC) systems. The aces-tmp tool is a temporary directory management tool that is part of the EasyBuild framework.
easybuild-faster Faster Software Framework Development & Optimization Tools Computer & Information Sciences Optimizes Software Build Process For Hpc Systems, Reduces Build Times, Improves Overall Efficiency, Works As An Extension Of Easybuild Hpc, Software Build Optimization, High-Performance Computing Faster: https://hprc.tamu.edu/software/faster/ Faster: 0 EasyBuild-Faster is an extension of EasyBuild, a software build and installation framework for high-performance computing (HPC) systems. EasyBuild-Faster focuses on optimizing the software build process to reduce build times and improve overall efficiency on HPC systems.
easybuild-faster-myeb Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 0
easybuild-faster-scratch Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 0
easybuild-faster-tmp Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 0
easysfs Anvil Tool Genomic Analysis Biological Sciences Population Genomics Genomics easySFS is a tool for the effective selection of population size projection for construction of the site frequency spectrum. edta: ed The software allows users to estimate basic population genetic parameters such as theta and Tajima's D, perform neutrality tests, and visualize and analyze the SFS data. Population Genomics, Genetic Analysis, Sfs Data Analysis Anvil: https://www.rcac.purdue.edu/software/easysfs Anvil: 1.0 easysfs is a software tool designed for population genomics analysis, specifically focusing on Site Frequency Spectrum (SFS) data.
ecbuild Aces, Faster Build System Generator Development Tools Earth & Environmental Sciences ECbuild is a CMake-based build system, consisting of a collection of CMake macros and functions that ease the managing of software build systems.
Description Source: https://github.com/ecmwf/ecbuild
Automated Generation Of Cmake-Based Build Systems, Configuration Management For Earth System Model Projects, Integration With Esm Workflows & Components, Facilitates Model Coupling & Parallel Execution Build System Generator, Earth System Model, Cmake-Based, Esm Project, Model Coupling, Parallel Execution https://github.com/ecmwf/ecbuild https://ecbuild.readthedocs.io/en/latest/ https://github.com/ecmwf/ecbuild/tree/develop/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.7.0, 3.8.0
Faster: 3.7.0, 3.8.0
ecBuild is a CMake-based build system generator for Earth system model (ESM) projects. It focuses on enabling easy configuration and management of complex ESM projects by automating the generation of build systems.
eccodes Aces, Faster Data Encoding/Decoding Data Processing Earth & Environmental Sciences Meteorology Atmospheric Sciences ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in different WMO formats.
Description Source: https://github.com/ecmwf/eccodes
1. Encode and decode GRIB data
2. Manipulate meteorological data
3. Support for various meteorological data formats
4. Extensive functionalities for data processing and analysis
Grib Data, Meteorology, Oceanography, Climatology https://confluence.ecmwf.int/display/ECC/ecCodes+Home https://confluence.ecmwf.int/display/ECC/Documentation https://confluence.ecmwf.int/display/ECC/API+examples
https://confluence.ecmwf.int/display/ECC/Training+material
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.24.2, 2.27.0, 2.31.0
Faster: 2.22.1, 2.24.2
eccodes is a software package for encoding/decoding and manipualting meteorological data in GRIB format. It provides a large number of functionalities to work with data in meteorology, oceanography, and climatology.
edlib Faster Bioinformatics Library Biological Sciences 1. Supports various alignment algorithms such as Edit distance, Hamming distance, and NW (Needleman-Wunsch) global alignment.
2. Provides functions for pairwise alignment of sequences and computing their similarity.
3. Includes methods for approximate string matching and searching.
4. Allows users to set custom parameters for alignment and scoring.
5. Written in C language with bindings available for Python and other programming languages.
Sequence Alignment, Edit Distance, Pairwise Alignment Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.3.8.Post1-Python-3.7.4 Edlib is an open-source library for sequence alignment using edit (Levenshtein) distance and pairwise alignment. It includes several alignment algorithms and methods for comparing sequences.
edta Anvil Tool Bioinformatics Biological Sciences Genetics Biological Sciences Edta is developed for automated whole-genome de-novo TE annotation and benchmarking the annotation performance of TE libraries. eggnog-mapper: eggnog- 1. De novo transcriptome assembly from RNA-Seq data
2. Reconstruction of full-length transcripts
3. Improvement of gene annotation
4. Identification of alternatively spliced isoforms
5. Estimation of expression levels
Transcriptome Assembly, RNA-Seq, Gene Annotation Anvil: https://www.rcac.purdue.edu/software/edta Anvil: 1.9.6, 2.0.0 EDTA (Enhanced De Novo Transcriptome Assembler) is a software tool designed for transcriptome assembly from RNA-Seq data. It aims to accurately reconstruct full-length transcripts and improve gene annotation.
eggnog-mapper Anvil Bioinformatics Tool Annotation Tool Biological Sciences Genomics Bioinformatics Eggnog-mapper is a tool for fast functional annotation of novel sequences. Functional Annotation Of Non-Model Species, Orthology-Based Methods, Gene Function Prediction Through Orthology Transfer Functional Annotation, Orthology, Gene Function Prediction Anvil: https://www.rcac.purdue.edu/software/eggnog-mapper Anvil: 2.1.7 EggNOG-mapper is a tool that allows functional annotation of non-model species using orthology-based methods. It leverages precomputed clusters of orthologous genes from multiple species to predict gene function through orthology transfer.
eigen Aces, Anvil, Darwin, Expanse, Faster, Stampede3 Linear Algebra Library Library Computer & Information Sciences Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Description Source: https://eigen.tuxfamily.org/index.php?title=Main_Page
1. Straightforward API for matrix operations
2. Support for dense and sparse matrices
3. Various linear algebra and numerical solvers
4. Eigenvalues and eigenvectors computations
5. Fast and efficient computation
Linear Algebra, Numerical Computation, C++ Library https://eigen.tuxfamily.org/ https://eigen.tuxfamily.org/dox/ https://eigen.tuxfamily.org/dox/GettingStarted.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/eigen
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 3.3.8, 3.3.9, 3.4.0
Anvil: 3.3.9
Expanse: Aoih524, Rarzo6S, ...
Faster: 3.3.7, 3.3.8, 3.3.9, 3.4.0
Stampede-3: 3.4.0
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
einops Aces, Faster Python Library Library Computer & Information Sciences Artificial Intelligence & Intelligent Systems Computer Science Einops is a python library which allows for Flexible and powerful tensor operations for readable and reliable code. Supports numpy, pytorch, tensorflow, jax, and others.
Description Source: https://github.com/arogozhnikov/einops
1. Simple and expressive syntax for tensor reshaping operations. 2. Supports various tensor operations like permutation, transpose, reduction, etc. 3. Integration with popular deep learning frameworks like PyTorch and TensorFlow. 4. Efficient and easy-to-understand code for tensor manipulations. Python Library, Tensor Manipulation, Deep Learning Frameworks https://einops.rocks/ https://einops.rocks/#api https://einops.rocks/1-einops-basics/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.4.1
Faster: 0.3.2, 0.4.1, 0.6.0
einops is a Python library for tensor operations and reshaping with a focus on readability and flexibility. It provides a more intuitive and concise way of manipulating tensor dimensions in deep learning frameworks.
elfutils Aces, Faster Utilities elfutils is a collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux.
Description Source: https://sourceware.org/elfutils/
1. Reading and analyzing ELF files
2. Modifying and updating ELF binaries
3. Debugging programs and libraries
4. Extracting and examining symbol tables and section headers
5. Inspecting and manipulating core dump files
6. Disassembling machine code
7. Handling DWARF debugging information
8. Checking and correcting ELF header information
Binary Tool, Elf Files, Debugging, Programming https://sourceware.org/elfutils/ https://github.com/roolebo/elfutils/blob/master/libelf/libelf.h https://access.redhat.com/documentation/en-us/red_hat_developer_toolset/7/html/user_guide/chap-elfutils Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.187, 0.189
Faster: 0.182, 0.185, 0.187, 0.189
elfutils is a collection of various binary tools for working with ELF files. It includes utilities for analyzing, manipulating, and creating programs and object files in the Executable and Linkable Format (ELF). These tools are commonly used by programmers, debuggers, and system administrators to inspect and modify ELF binaries.
elpa Aces, Expanse, Faster, Ookami Library Numerical Library Computer & Information Sciences The publicly available ELPA library provides highly efficient and highly scalable direct eigensolvers for symmetric (hermitian) matrices. Descripiton Source:https://elpa.mpcdf.mpg.de/ABOUT_ELPA.html Solves Standard & Generalized Eigenvalue Problems For Dense Hermitian Matrices, Optimized For High-Performance Computing Systems, Utilizes Highly Scalable Algorithms For Efficiency, Suitable For Parallel Computing Linear Algebra, Eigenvalue Problems, High-Performance Computing, Scalable Algorithms https://elpa.mpcdf.mpg.de/ https://elpa.mpcdf.mpg.de/documentation/doxygen/ELPA_DOXYGEN_PAGES/ELPA-2024.03.001.rc1/html/index.html https://gitlab.mpcdf.mpg.de/elpa/elpa/-/blob/master/documentation/USERS_GUIDE.md Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2021.11.001, 2022.05.001-Cuda-11.8.0, 2022.05.001, 2023.05.001
Expanse: Eq4324U, Fyc633Z
Faster: 2021.05.001, 2021.11.001, 2022.05.001Cuda-11.8.0
Ookami: 2016.11.001.Pre
ELPA (Eigenvalue SoLvers for Petaflop Applications) is a library for solving the standard and generalized eigenvalue problems for dense Hermitian matrices. It is designed for high-performance computing systems and utilizes highly scalable algorithms to achieve high efficiency.
emacs Aces, Anvil, Darwin Text Editor Productivity Tool Computer & Information Sciences GNU Emacs is an extensible, customizable, free/libre text editor.
Description Source: https://www.gnu.org/savannah-checkouts/gnu/emacs/emacs.html
Emacs offers a range of features like syntax highlighting, auto-indentation, content-aware editing, integrated version control, and a large collection of plugins and packages (e.g., Org mode for organizing notes and tasks). It supports various programming languages and can be customized using Emacs Lisp. Text Editor, Customizable, Extensible, Self-Documenting https://www.gnu.org/software/emacs/ https://www.gnu.org/software/emacs/manual/html_node/emacs/index.html https://www.gnu.org/software/emacs/manual/html_node/emacs/Basic.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/emacs
Aces: 27.2, 28.2
Anvil: 27.2
Emacs is a highly customizable, extensible, and self-documenting text editor. It is known for its powerful editing capabilities, which include content-aware editing, syntax highlighting, and a wide range of plugins and extensions.
emboss Anvil, Expanse, Faster Analysis Tool Sequence Analysis Tools Biological Sciences Sequence Analysis Bioinformatics Emboss is 'The European Molecular Biology Open Software Suite' Sequence Alignment, Database Searching, Motif Identification, Pattern Matching, Phylogenetic Analysis Bioinformatics, Computational Biology, Sequence Analysis, Biological Data Anvil: https://www.rcac.purdue.edu/software/emboss
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 6.6.0
Expanse: 6.6.0
Faster: 6.6.0-Java-13, 6.6.0
EMBOSS is a comprehensive software analysis package for biological sequence data. It provides over 200 tools for sequence alignment, database searching, pattern matching, motif identification, and more. EMBOSS is widely used in bioinformatics and computational biology research.
enchant-2 Aces, Faster Spellchecking Spellchecking Library Computer & Information Sciences Enchant aims to provide a simple but comprehensive abstraction for dealing with different spell checking libraries in a consistent way. A client, such as a text editor or word processor, need not know anything about a specific spell-checker, and since all back-ends are plugins, new spell-checkers can be added without needing any change to the program using Enchant. 1. Cross-platform spellchecking capabilities. 2. Consistent API for invoking spellchecking routines. 3. Supports multiple backends for spellchecking. 4. Customizable dictionaries and language support. Spellchecking, Library, Cross-Platform, Spellchecking Routines Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.3.3
Faster: 2.3.3
Enchant is a spellchecking library that provides a consistent API for invoking spellchecking routines across different platforms. Enchant-2 is the newer version of the Enchant spellchecking framework.
energyplus Faster Simulation Software Building Performance Simulation Engineering & Technology Building Energy Efficiency Environmental Engineering Detailed Building Energy & Environmental Simulation, Support For Various Hvac Systems & Control Strategies, Advanced Fenestration Modeling Capabilities, Weather Data Integration For Accurate Simulations, Parametric Analysis & Optimization Features Energy Simulation, Building Performance, Environmental Control, Parametric Analysis, Building Energy Consumption Faster: https://hprc.tamu.edu/software/faster/ Faster: 9.3.0, 23.1.0 EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption and water use in buildings. It allows users to evaluate the combined performance of building energy and environmental control systems.
ensembl-vep Anvil Bioinformatics Sciences Biology VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
Description Source: https://useast.ensembl.org/info/docs/tools/vep/index.html
https://useast.ensembl.org/info/docs/tools/vep/index.html https://useast.ensembl.org/info/docs/tools/vep/script/index.html#contents https://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html
https://useast.ensembl.org/info/docs/tools/vep/script/vep_example.html
Anvil: https://www.rcac.purdue.edu/software/ensembl-vep Anvil: 106.1, 107.0, 108.2
entrezdirect Expanse Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. https://github.com/Klortho/edirect https://www.ncbi.nlm.nih.gov/books/NBK179288/ https://www.ncbi.nlm.nih.gov/books/NBK565821/
https://hpc.nih.gov/apps/edirect.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: U7Oel2N, ...
epic2 Anvil Data Analysis Tool Bioinformatics Tool Biological Sciences Genomics Bioinformatics epic2 is an ultraperformant Chip-Seq broad domain finder based on SICER. 1. Efficient identification of enriched genomic regions in large ChIP-seq datasets.
2. High sensitivity and specificity in peak calling.
3. User-friendly interface for ease of use.
4. Capable of handling large-scale data analysis.
Chip-Seq, Peak Calling, Genomic Regions Anvil: https://www.rcac.purdue.edu/software/epic2 Anvil: 0.0.51, 0.0.52 epic2 is a software tool for identifying genomic regions enriched with ChIP-seq signal. It is specifically designed for identifying enriched regions in large datasets, offering high sensitivity and specificity in peak calling.
esm Faster Simulation Tool Modeling Software Earth & Environmental Sciences Earth System Modeling, Climate Variability & Change Simulation, Environmental Process Analysis, Atmosphere-Ocean-Land Interactions Earth System Modeling, Climate Simulation, Environmental Processes, Earth System Interactions Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.0.0 ESM (Earth System Modeling) is a software tool designed for simulating and studying complex interactions within the Earth system, including the atmosphere, oceans, land surface, and cryosphere. It enables researchers to investigate climate variability, climate change, and environmental processes.
esmf Aces, Expanse, Faster Computational Software Modeling Framework Physical Sciences Atmospheric Sciences Earth & Environmental Sciences The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. Such applications may include a few or dozens of components representing atmospheric, oceanic, terrestrial, or other physical domains, and their constituent processes (dynamical, chemical, biological, etc.).
Description Source: https://earthsystemmodeling.org/docs/release/latest/ESMF_usrdoc/node2.html
Supports Modeling Weather, Climate, & Earth Science Phenomena, Provides Infrastructure For Building & Coupling Models, Facilitates Interoperability & Data Exchange Between Models, Offers Tools For Parallel Computing & Performance Optimization Earth System Modeling, Climate Modeling, Weather Modeling, Model Coupling, Earth Science https://earthsystemmodeling.org/ https://earthsystemmodeling.org/doc/ https://earthsystemmodeling.org/tutorials/ Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.0.1, 8.1.1, 8.3.0
Expanse: Nvkj3Wb
Faster: 8.1.1, 8.2.0, 8.3.0
The Earth System Modeling Framework (ESMF) is a software infrastructure for building and coupling weather, climate, and related Earth science models. It provides a flexible and reusable software architecture that facilitates the use, development, and coupling of Earth science models.
evidencemodeler Anvil Pipeline Gene Prediction Tool Biological Sciences Genomics Bioinformatics Evidencemodeler is a software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. exonerat Combines Evidence From Multiple Sources To Generate Accurate Gene Structures, Supports Integration Of Predicted Gene Models, Transcriptome Alignments, Protein Homology Evidence, & More, Allows Customization Of Evidence Weightings & Parameters For Gene Structure Prediction, Ability To Incorporate User-Defined Gene Models & Evidence Sources Gene Prediction, Annotation, Bioinformatics, Transcriptomics, Genomics Anvil: https://www.rcac.purdue.edu/software/evidencemodeler Anvil: 1.1.1 EvidenceModeler (EM) is a flexible and customizable pipeline for generating gene structure annotations by integrating evidence from various prediction programs and transcriptomic data.
exabayes Expanse Phylogenetic Software Bioinformatics Biological Sciences Evolutionary Biology Ecology ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters. ExaBayes offers efficient and scalable Markov chain Monte Carlo (MCMC) algorithms for analyzing very large Bayesian phylogenetic datasets. It is specifically designed to handle massive datasets on high-performance computing (HPC) systems. The software supports various models of sequence evolution and tree priors, enabling complex phylogenetic analyses. ExaBayes leverages GPU acceleration for rapid computation and supports MPI for parallel processing. Bayesian Inference, Phylogenetics, Parallel Computing, Mcmc, Hpc Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 1.5.1 ExaBayes is a software package for Bayesian inference on large phylogenetic trees using parallel computing techniques.
exiv2 Aces, Faster Metadata Management Library, Utility Computer & Information Sciences Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata. 1. Supports reading and writing Exif metadata in various image formats
2. Supports reading and writing IPTC and XMP metadata
3. Command-line utility for batch processing of image metadata
4. Embeds, extracts, and deletes metadata from images
5. Supports various image formats including JPEG, TIFF, PNG, and more
Metadata Management, Image Processing, Command-Line Utility Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.27.5
Faster: 0.27.5
Exiv2 is a C++ library and a command-line utility to manage image metadata. It provides fast and easy read and write access to the Exif, IPTC, and XMP metadata of images in various formats.
exonerate Anvil Bioinformatics Tool Sequence Alignment Biological Sciences Genomics Bioinformatics Exonerate is a generic tool for pairwise sequence comparison/alignment. Flexible Sequence Alignment & Homology Search Algorithms, Support For Protein-Protein, DNA-DNA, Protein-DNA, & Est-Genome Alignments, Ability To Handle Large Genomic Datasets Efficiently, Customizable Scoring Parameters For Alignment, Output In Various Formats For Downstream Analysis Sequence Alignment, Homology Search, Bioinformatics, Genomics Anvil: https://www.rcac.purdue.edu/software/exonerate Anvil: 2.4.0
Faster: 2.4.0
Exonerate is a versatile tool for sequence alignment and homology search. It is widely used for comparison of protein and nucleotide sequences against a wide range of genomic databases.
expansionhunter Anvil Data Analysis Tool Bioinformatics Biological Sciences Medical Biotechnology Genetics Expansion Hunter: a tool for estimating repeat sizes. Detection Of Repeat Expansions In Human Genomes, Identification Of Repeat Length Differences Linked To Genetic Diseases, Visualization Tools For Variant Interpretation, Analysis Of Whole Genome Sequencing Data Genetic Diseases, Repeat Expansions, Variant Interpretation, Whole Genome Sequencing Anvil: https://www.rcac.purdue.edu/software/expansionhunter Anvil: 4.0.2 ExpansionHunter is a set of tools for detecting repeat expansions in whole genome sequencing data. It is specifically designed to identify repeat length differences that are associated with genetic diseases. ExpansionHunter scans the genome for such expansions and provides detailed information and visualizations to assist in variant interpretation.
expat Aces, Faster, Kyric Xml Parser Library Computer & Information Sciences Expat is a stream-oriented XML parser library written in C and excels with files too large to fit RAM, and where performance and flexibility are crucial.
Description Source: https://libexpat.github.io/
1. Supports parsing of XML documents
2. Provides API for developers to implement XML parsing in their applications
3. Fast and efficient parsing of XML
4. Easy to integrate with various programming languages
Xml Parser, Library https://libexpat.github.io/ https://libexpat.github.io/doc/api/latest/ https://libexpat.github.io/doc/getting-started/
https://www.xml.com/pub/1999/09/expat/index.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.2.9, 2.4.1, 2.4.8, 2.4.9, 2.5.0
Faster: 2.2.5, 2.2.7, 2.2.9, 2.4.1, 2.4.8, 2.4.9, 2.5.0
Expat is an XML parser library written in C. It is a fast and lightweight library that is designed for high-performance applications.
expecttest Aces, Faster Automation Tool Testing Tool This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output.
Description Source: https://github.com/ezyang/expecttest
Automating Interactive Applications, Scripting Language For Testing, Automation Of System Administration Tasks Testing Tool, Automation, Scripting, Software Development https://github.com/ezyang/expecttest https://github.com/ezyang/expecttest/blob/main/README.md Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.1.3, 0.1.5
Faster: 0.1.3, 0.1.5
expecttest is a versatile testing tool for software developers that allows for the automation of interactive applications, system administration tasks, and more. It provides a simple scripting language for driving applications and processes under test, making it easy to automate testing workflows.
extrae Kyric Tool Performance Analysis Computer & Information Sciences, Software Engineering, Systems, & Development, Engineering & Technology, Training, Infrastructure & Instrumentation Capture & Analyze Trace Data From Parallel Applications, Identify Performance Bottlenecks, Optimize Application Performance, Monitor Application Behavior Performance Analysis, Trace Data, Parallel Applications, Distributed Applications https://tools.bsc.es/extrae https://tools.bsc.es/doc/html/extrae/api.html https://tools.bsc.es/doc/html/extrae/quick-guide.html
https://tools.bsc.es/doc/html/extrae/examples.html
Kyric: 3.7.0 Extrae is a performance analysis tool designed to capture and analyze trace data from parallel and distributed applications. It allows users to monitor and examine the behavior of their applications in terms of performance, identifying potential bottlenecks and areas for optimization.
eztrace Aces Library Tool Performance Analysis Tool Computer & Information Sciences EZTrace is a tool that aims at generating automatically execution trace from HPC programs. 1. Tracing function calls and communication patterns
2. Performance analysis
3. Execution characteristics monitoring
4. Profiling applications
Performance Analysis, Function Call Tracing, Profiling, Monitoring Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.1 eztrace is a tool that provides a set of library calls that can be used to trace the evolution of applications during their execution. It helps in performance analysis by collecting information about function calls, communication patterns, and execution characteristics.
fasta3 Anvil Sequence Analysis Tool Bioinformatics Tool Biological Sciences Fasta3 is a suite of programs for searching nucleotide or protein databases with a query sequence. fasta3 includes tools for database searching, sequence alignment, and motif finding. It provides efficient methods for comparing DNA or protein sequences. Bioinformatics, Sequence Analysis, Alignment Anvil: https://www.rcac.purdue.edu/software/fasta3 Anvil: 36.3.8 fasta3 is a suite of tools for searching nucleotide or protein databases with a query sequence, as well as for conducting multiple sequence alignment.
fastai Aces Machine Learning Framework Libraries Computer & Information Sciences Machine Learning, Deep Learning Artificial Intelligence & Intelligent Systems fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance.
Description Source: https://docs.fast.ai/#about-fastai
1. High-level API for training deep learning models. 2. Implements cutting-edge techniques in an accessible way. 3. Provides pre-trained models for transfer learning. 4. Includes tools for interpretability and visualization. Deep Learning, Neural Networks, Machine Learning, Pytorch https://www.fast.ai/ https://docs.fast.ai/ https://course.fast.ai/
https://course.fast.ai/Lessons/part2.html
https://course18.fast.ai/lessonsml1/lesson1.html
https://www.youtube.com/playlist?list=PLfYUBJiXbdtSLBPJ1GMx-sQWf6iNhb8mM
Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.7.10 The fastai library simplifies training fast and accurate neural networks using modern best practices. It is built on top of PyTorch and provides many high-level abstractions to make it easy to train state-of-the-art models with little code.
fastani Anvil, Bridges-2 Genome Analysis Tool Bioinformatics Tool Biological Sciences Genomics Biology FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
Description Source: https://github.com/ParBLiSS/FastANI
1. Calculation of average nucleotide identity (ANI) between microbial genomes. 2. Utilizes MinHash algorithm for fast ANI estimation. 3. Supports large-scale genome comparisons efficiently. 4. Provides a rapid alternative to traditional ANI calculation methods. Bioinformatics, Genome Comparison, Bacterial Genomes https://github.com/ParBLiSS/FastANI https://github.com/ParBLiSS/FastANI/blob/master/README.md https://hackmd.io/@AstrobioMike/Nadjet-fastANI-example Anvil: https://www.rcac.purdue.edu/software/fastani
Bridges-2: https://www.psc.edu/resources/software/fastani
Anvil: 1.32, 1.33
Bridges-2: 1.33
fastANI is a tool for computing average nucleotide identity (ANI) and relatedness between bacterial and archaeal genomes at high speed. It uses MinHash to estimate ANI values in a fraction of the time compared to traditional methods.
fastcore Faster Python Library Library Computer & Information Sciences Provides Core Functions & Classes For Python Programming, Includes Utilities For Data Manipulation & Functional Programming, Optimizes General-Purpose Tasks For Improved Productivity Python Library, Utility Library, Data Manipulation, Functional Programming Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.3.27 fastcore is a utility library that provides a set of core functions and classes to improve the productivity and readability of Python code. It includes various utilities for data manipulation, functional programming, and general-purpose task optimization.
fastp Anvil, Expanse Tool Data Processing Biological Sciences Genomics Bioinformatics Fastp is an ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging, etc). The core features of fastp include adapter trimming, quality filtering, quality control, and error correction of sequencing data. Bioinformatics, Sequencing, Data Processing Anvil: https://www.rcac.purdue.edu/software/fastp
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 0.20.1, 0.23.2
Expanse: Vihdvcu
fastp is a tool designed for pre-processing high throughput sequencing data faster and more efficiently.
fastq_pair Anvil Data Processing Tool Bioinformatics Tool Biological Sciences Fastq_pair is used to match up paired end fastq files quickly and efficiently. Pairing & Sorting Paired-End Reads In Fastq Format, Efficient Processing Of Large Volumes Of Sequencing Data, Identification Of Matching Read Pairs, Organization Of Paired-End Reads For Downstream Analysis Bioinformatics, Computational Biology, Sequencing Data, Paired-End Reads, Fastq Format Anvil: https://www.rcac.purdue.edu/software/fastq_pair Anvil: 1.0 fastq_pair is a tool for pairing and sorting paired-end reads in FASTQ format. It is designed to efficiently process large volumes of paired-end sequencing data by identifying matching read pairs and organizing them for downstream analysis.
fastq-scan Anvil Bioinformatics Ngs Quality Control Biological Sciences Genomics Genetics Fastq-scan reads a FASTQ from STDIN and outputs summary statistics (read lengths, per-read qualities, per-base qualities) in JSON format. Batch Scanning Of Fastq Files, Quality Control Metrics Extraction For Ngs Data, Efficient Processing Of Large Datasets Ngs Data Analysis, Quality Control, Fastq File Processing Anvil: https://www.rcac.purdue.edu/software/fastq-scan Anvil: 1.0.0 fastq-scan is a tool for batch scanning and processing FASTQ files to extract quality control metrics for Next-Generation Sequencing (NGS) data.
fastq-tools Bridges-2 Data Processing Tool Command-Line Tools Biological Sciences Genomics Bioinformatics Small utilities for working with fastq sequence files. Some of the core features of fastq-tools include quality assessment, adapter trimming, filtering by quality scores, file format conversion, and extraction of specific sequences from FASTQ files. It aims to streamline common preprocessing tasks in next-generation sequencing data analysis pipelines. Bioinformatics, Ngs, Genome Sequencing, Sequence Analysis Bridges-2: https://www.psc.edu/resources/software/fastq-tools Bridges-2: 0.8 fastq-tools is a collection of simple and efficient command-line tools for processing FASTQ files commonly used in bioinformatics. It provides various utilities for quality control, filtering, and manipulation of raw sequencing data in FASTQ format.
fastqc Aces, Anvil, Bridges-2, Expanse, Faster Analysis Tool Quality Control Tool Biological Sciences Sciences Biology FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. Whereas Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems which were generated by the sequencer itself.
Description Source: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/1%20Introduction/1.1%20What%20is%20FastQC.html
Generate Quality Control Reports For Sequencing Data, Identify Potential Sequencing Errors & Biases, Visualize Sequence Quality Scores, Per Base Sequence Content, Gc Content, Sequence Duplication Levels, & More, Supports Various Sequencing Platforms & Data Formats Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ https://www.youtube.com/watch?v=bz93ReOv87Y Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/fastqc
Bridges-2: https://www.psc.edu/resources/software/fastqc
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.11.9-Java-11
Anvil: 0.11.9, 0.12.1
Bridges-2: 0.11.9
Expanse: 0.11.7
Faster: 0.11.9-Java-11
FastQC is a quality control tool for high throughput sequence data. It provides a detailed overview of the quality and potential issues in sequencing data generated by high throughput sequencing pipelines.
fastspar Anvil Computational Software Python Library Biological Sciences Fastspar is a tool for rapid and scalable correlation estimation for compositional data. fastspar provides a quicker alternative to SparCC, especially for large datasets, by utilizing an improved algorithm for computing compositional correlation values. It is designed to handle high-dimensional and sparse data typically encountered in microbiome research. Microbiome, Correlation, Compositional Data Anvil: https://www.rcac.purdue.edu/software/fastspar Anvil: 1.0.0 fastspar is a Python package that implements a fast version of SparCC, a correlation method tailored for compositional data commonly found in microbiome studies.
faststructure Anvil Inference Tool Population Structure Inference Biological Sciences Population Genetics Genetics fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. Population Structure Inference, Analysis Of Large Snp Genotype Data, Ability To Handle Datasets With Admixture Population Genetics, Structural Biology, Genomics Anvil: https://www.rcac.purdue.edu/software/faststructure Anvil: 1.0-Py27 faststructure is a software package for inferring population structure from large SNP genotype data. It is designed to work efficiently with large datasets and can identify population structure in the presence of admixture.
fasttree Aces, Anvil, Expanse Bioinformatics Tool Phylogenetic Tree Inference Biological Sciences Phylogenetics Bioinformatics FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7. Inference Of Approximately-Maximum-Likelihood Phylogenetic Trees, Support For Both Nucleotide & Protein Sequences, Efficient Handling Of Alignments With Thousands Of Sequences, Speed Optimization For Large-Scale Datasets Phylogenetics, Bioinformatics, Computational Biology, Sequence Analysis Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/fasttree
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Aces: 2.1.11
Anvil: 2.1.10, 2.1.11
Expanse: 2.1.10
Faster: 2.1.11
FastTree is a tool for inferring approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a few thousand sequences and has been designed to make trees with the minimum scale up to 100,000 sequences faster by approximating maximum-likelihood with heuristics.
fastx_toolkit Anvil Pre-Processing Tool Bioinformatics Tools Biological Sciences Sciences Biology The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Description Source: http://hannonlab.cshl.edu/fastx_toolkit/
The toolkit includes programs to filter, modify, and manipulate short-reads and perform various quality control checks on the FastQ files. Bioinformatics, Short-Reads, Preprocessing http://hannonlab.cshl.edu/fastx_toolkit/ http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_info_example Anvil: https://www.rcac.purdue.edu/software/fastx_toolkit Anvil: 0.0.14 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fastx-toolkit Anvil, Bridges-2, Expanse Tool Data Processing & Analysis Biological Sciences Sciences Biology The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Description Source: http://hannonlab.cshl.edu/fastx_toolkit/
Quality Filtering Of Fastq Files, Adapter Trimming, Format Conversion Between Fasta & Fastq Files, Length Filtering, Sequence Preprocessing Bioinformatics, Ngs Data Processing, Sequence Analysis, Fastq Manipulation http://hannonlab.cshl.edu/fastx_toolkit/ http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastq_info_example Anvil: https://www.rcac.purdue.edu/software/fastx-toolkit
Bridges-2: https://www.psc.edu/resources/software/fastx-toolkit
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 0.0.14
Bridges-2: 0.0.14
Expanse: 0.0.14
The fastx-toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. The tools simplify and streamline various tasks related to quality control, adapter trimming, and format conversion of next-generation sequencing data.
fdasrsf Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.3.12
femzip-l Faster Tool Data Compression Engineering & Technology Computational Sciences Engineering & Technology 1. Lossless compression of Finite Element Models (FEM) data.
2. Reduction of storage space required for FEM data.
3. Maintains the accuracy and integrity of the model throughout the compression process.
Compression, Finite Element Models, Engineering, Computational Sciences Faster: https://hprc.tamu.edu/software/faster/ Faster: 10.73 femzip-l is a lossless compression tool designed specifically for Finite Element Models (FEM) in engineering and computational sciences. It aims to reduce the storage space required for FEM data without compromising on the accuracy and integrity of the model.
ffmpeg Aces, Anvil, Bridges-2, Expanse, Faster, Ookami Tool Utility Engineering & Technology FFmpeg is a collection of libraries and tools to process multimedia content such as audio, video, subtitles and related metadata.
Description Source: https://github.com/FFmpeg/FFmpeg
Encoding, Decoding, Transcoding, Muxing, Demuxing, Streaming, Filtering, & Playing Audio/Video Files, Support For A Wide Range Of Codecs, Formats, & Protocols, Cross-Platform Compatibility Media Processing, Multimedia, Video, Audio https://www.ffmpeg.org/ https://www.ffmpeg.org/documentation.html https://trac.ffmpeg.org/wiki/Encode/H.264
https://trac.ffmpeg.org/wiki
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/ffmpeg
Bridges-2: https://www.psc.edu/resources/software/ffmpeg
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 4.3.2, 4.4.2, 5.1.2, 6.0
Anvil: 4.2.2
Bridges-2: 4.3.1
Expanse: Vac6D7F, W7Ehiyr
Faster: 4.2.2, 4.3.1, 4.3.2, 4.4.2, 5.0.1, 5.1.2, 6.0
Ookami: 5.1
FFmpeg is a free and open-source software project consisting of a large suite of libraries and programs for handling video, audio, and other multimedia files and streams.
ffnvcodec Aces, Faster Library Codec Library Computer & Information Sciences FFmpeg version of headers required to interface with Nvidias codec APIs.
Description Source: https://github.com/FFmpeg/nv-codec-headers
1. Hardware-accelerated video encoding and decoding with NVIDIA GPUs
2. Support for popular video codecs such as H.264 and HEVC
3. High-performance video processing
4. Integration with NVIDIA CUDA technology for parallel processing
Codec, Video Processing, Gpu Acceleration https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git https://git.videolan.org/?p=ffmpeg/nv-codec-headers.git;a=tree Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 11.1.5.2, 12.0.16.0
Faster: 11.1.5.2, 12.0.16.0
ffnvcodec is a codec library provided by NVIDIA for efficient video encoding and decoding using the NVIDIA GPU hardware acceleration.
fftw Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Kyric Computational Software Library Mathematics Numerical Analysis Applied Mathematics FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.
Description Source: https://www.fftw.org/
1. Efficient DFT computation in multiple dimensions.
2. Supports both real and complex data.
3. High performance through optimized algorithms and implementations.
4. Portable and easy-to-use interface.
5. Scalable to large input sizes.
Signal Processing, Data Compression, Partial Differential Equations https://www.fftw.org/ https://www.fftw.org/fftw3_doc/ https://www.fftw.org/fftw3_doc/Tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/fftw
Bridges-2: https://www.psc.edu/resources/software/fftw
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.8, 3.3.9, 3.3.10
Anvil: 2.1.5, 3.3.8
Bridges-2: 3.3.8
Delta: 3.3.10
Expanse: Bmvqsbr, Cesmlwb, ...
Faster: 3.3.8, 3.3.9, 3.3.10
FFTW is a fast C library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is widely used in areas such as signal processing, data compression, and solving partial differential equations.
fftw.mpi Aces, Faster Tool Computational Mathematics Mathematics Engineering FFTW.mpi is a part of the FFTW (Fastest Fourier Transform in the West) library that specializes in performing highly efficient, parallel Fast Fourier Transforms (FFTs) using MPI (Message Passing Interface) for distributed-memory computing environments. This extension enables the library to handle large-scale FFT computations across multiple processors in a cluster, optimizing performance for applications in engineering, physics, and other scientific fields that require processing large datasets or complex numerical simulations. The mpi version of FFTW provides parallel computing capabilities using the Message Passing Interface (MPI) standard, enabling high-performance computations of Fourier transforms across distributed computing resources. This allows for efficient processing of large datasets and complex simulations in parallel. Computational Software, Hpc Tools https://www.fftw.org/fftw3_doc/Distributed_002dmemory-FFTW-with-MPI.html#Distributed_002dmemory-FFTW-with-MPI https://www.fftw.org/fftw3_doc/FFTW-MPI-Reference.html https://www.fftw.org/fftw3_doc/Using-MPI-Plans.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.10
Faster: 3.3.10
FFTW is a comprehensive collection of fast C routines for computing the Discrete Fourier Transform (DFT) and various generalizations, used in a wide range of applications in computational mathematics, physics, and engineering.
fftw3 Ookami, Stampede3 Numerical Library Library Physical Sciences Computational Physics Condensed Matter Physics FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). We believe that FFTW, which is free software, should become the FFT library of choice for most applications.
Description Source: https://www.fftw.org/
1. Efficient computation of discrete Fourier transforms (DFTs)
2. Support for various transform sizes and data types
3. Thread-safe and parallelized algorithms for performance optimization
4. Portability across different platforms
5. Customizable with user-defined options and configurations
Fft, Fourier Transform, Open-Source, Computational Physics https://www.fftw.org/ https://www.fftw.org/fftw3_doc/ https://www.fftw.org/fftw3_doc/Tutorial.html Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Ookami: Gcc12/Openmpi4.1.4/3.3.10
Stampede-3: 3.3.10
The Fastest Fourier Transform in the West (FFTW) is an open-source software library for calculating discrete Fourier transforms (DFTs) efficiently. It provides a wide range of algorithms for executing Fourier transforms of various sizes, both real and complex data.
fiji Faster Analysis Tool Image Processing Software Other Natural Sciences Key features of Fiji include a user-friendly interface, support for a wide range of image file formats, a large collection of built-in plugins for image enhancement and analysis, customizable scripting with a macro language, and the ability to create custom plugins. Image Processing, Scientific Research, Image Analysis Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.9.0 Fiji is an image processing package, a distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. It is open-source software extensively used in scientific research for image visualization and processing.
file Aces, Faster Command Line Tool Utility The file command is "a file type guesser", that is, a command-line tool that tells you in words what kind of data a file contains.
Description Source: https://www.darwinsys.com/file/
Identifying File Types, Determining File Content File Management, Command-Line Utility https://www.darwinsys.com/file/ https://linux.die.net/man/1/file https://man7.org/linux/man-pages/man1/file.1.html#EXAMPLES Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.43
Faster: 5.38, 5.43
File is a command-line utility that performs file type identification. It is commonly used to determine the file type and content of a given file or set of files.
filtlong Anvil Data Filtering Tool Sequence Data Analysis Biological Sciences Genetics Biological Sciences Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. Filtering Of Long Reads, Supports Pacbio & Oxford Nanopore Sequencing Data, Option To Specify Length Or Quality Thresholds For Filtering Bioinformatics, Long Read Sequencing, Sequence Data Processing Anvil: https://www.rcac.purdue.edu/software/filtlong Anvil: 0.2.1 filtlong is a tool for filtering long reads generated by third-generation sequencing technologies such as PacBio or Oxford Nanopore. It allows for the removal of reads based on user-defined length or quality thresholds.
fiona Aces, Faster Library Data Processing & Visualization Earth & Environmental Sciences Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely. Support For Various Gis File Formats Such As Shapefile, Geojson, Kml, Gpkg, & Others, Integration With Ogr (Simple Features Library) For Efficient Data Access, Ability To Read & Write Vector Data With Support For Geometry Manipulation, Designed For Easy Interaction With Geospatial Data In Python Applications Python Library, Geospatial Data, Gis, Vector Data Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.8.21, 1.9.2, 1.9.5
Faster: 1.8.16-Python-3.8.2, 1.8.20, 1.8.21, 1.9.5
Fiona is a Python library for reading and writing geospatial vector data formats.
firefox Aces, Faster Web Browser Web Browser Computer & Information Sciences Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. Cross-Platform Web Browser, Open-Source Software, Highly Customizable With Add-Ons & Themes, Enhanced Privacy Features Like Tracking Protection, Built-In Password Manager & Popup Blocker, Frequent Updates For Security & Performance Improvements Web Browser, Internet, Privacy, Open-Source, Cross-Platform https://www.mozilla.org/en-US/firefox/new/ https://developer.mozilla.org/en-US/docs/Mozilla/Firefox https://developer.mozilla.org/en-US/docs/Learn Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 118.0.2, 124.0.1
Faster: 44.0.2, 114.0B9, 118.0.2
Mozilla Firefox, commonly known as Firefox, is a free and open-source web browser developed by the Mozilla Foundation and its subsidiary, Mozilla Corporation. It is available for Windows, macOS, Linux, and mobile devices. Firefox focuses on privacy, speed, and customization.
firestarter Faster Security Tool Firewall Configuration Tool Computer & Information Sciences Graphical Interface For Managing Firewall Settings, Ability To Set Up Rules For Incoming & Outgoing Traffic, Monitoring Of Network Connections, Support For Nat Configurations, Logging & Reporting Features Firewall, Network Security, Linux Faster: https://hprc.tamu.edu/software/faster/ Faster: 2.0 Firestarter is a visual firewall tool that allows users to configure a firewall for Linux systems using an easy-to-use graphical interface. It provides a user-friendly way to manage network security policies and rules.
flac Aces, Faster Compression Tool Audio Processing Other Computer & Information Sciences FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
Description Source: https://xiph.org/flac/
Lossless compression of audio files, preservation of original audio quality, support for metadata tagging, seeking, and error detection Audio Codec, Open-Source, Lossless Compression https://xiph.org/flac/ https://xiph.org/flac/api/index.html https://github.com/xiph/flac/tree/master/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.3.3, 1.3.4, 1.4.2
Faster: 1.3.3, 1.3.4, 1.4.2
Free Lossless Audio Codec (FLAC) is an open-source audio coding format for lossless compression of digital audio. It offers high audio quality and smaller file sizes without losing any information during compression and decompression.
flash Bridges-2, Faster Computational Physics Simulation Software Physical Sciences Fluid & Plasma Physics Physical Sciences FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
Description Source: https://ccb.jhu.edu/software/FLASH/
Flash provides a comprehensive suite of tools for solving complex partial differential equations, supporting various physical models and simulation methodologies. It offers advanced meshing capabilities, parallel computing support, visualization tools, and post-processing features. Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis https://ccb.jhu.edu/software/FLASH/ https://sourceforge.net/p/flashpage/code/ci/master/tree/ https://sourceforge.net/p/flashpage/code/ci/master/tree/flash.c Bridges-2: https://www.psc.edu/resources/software/flash
Faster: https://hprc.tamu.edu/software/faster/
Bridges-2: 1.2.11
Faster: 2.2.00
Flash is a multi-purpose computational software that specializes in numerical simulations for fluid dynamics, electromagnetics, structural analysis, and other physics-based applications. It is developed and maintained by the Center for Computational Sciences and Engineering at Lawrence Berkeley National Laboratory.
flask Aces, Faster Open Source Web Framework Computer & Information Sciences Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications.
Description Source: https://palletsprojects.com/p/flask/
Quick & Easy To Set Up & Get Started, Minimalistic Design With A Simple & Straightforward Api, Extensible Through A Variety Of Plugins & Extensions, Built-In Development Server & Debugger, Support For Secure Cookies & Sessions, Jinja2 Template Engine For Efficient Html Rendering, Werkzeug Wsgi Toolkit For Handling Requests & Responses Web Development, Python, Framework, Web Applications https://palletsprojects.com/p/flask/ https://flask.palletsprojects.com/en/3.0.x/ https://flask.palletsprojects.com/en/3.0.x/tutorial/
https://www.tutorialspoint.com/flask/index.htm
https://www.fullstackpython.com/flask.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.1.2, 2.2.2
Faster: 1.1.2, 2.0.2, 2.2.2
Flask is a lightweight and versatile Python web application framework that provides the essentials for building web applications. It is known for its simplicity, flexibility, and ease of use, making it a popular choice for developers.
flatbuffers Aces, Faster Library Serialization Library Computer & Information Sciences FlatBuffers is a cross platform serialization library architected for maximum memory efficiency. It allows you to directly access serialized data without parsing/unpacking it first, while still having great forwards/backwards compatibility.
Description Source: https://github.com/google/flatbuffers/
Efficient Data Serialization & Deserialization, Cross-Platform Support, Customizable Data Schemas, Random Access To Serialized Data, Minimal Memory Allocation & Copying Serialization, Data Storage, Communication, Efficiency, Cross-Platform https://github.com/google/flatbuffers https://flatbuffers.dev/modules.html https://flatbuffers.dev/flatbuffers_guide_tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.12.0, 2.0.0, 2.0.7, 23.1.4, 23.5.26
Faster: 1.12.0, 2.0.0, 2.0.7, 23.1.4
FlatBuffers is an open-source, cross-platform serialization library for efficient data storage and communication. It allows for storing and accessing serialized data without parsing and generating overhead, making it faster and more memory-efficient than traditional serialization methods.
flatbuffers-python Aces, Faster Library FlatBuffers is a cross platform serialization library architected for maximum memory efficiency. It allows you to directly access serialized data without parsing/unpacking it first, while still having great forwards/backwards compatibility.
Description Source: https://github.com/google/flatbuffers/
https://pypi.org/project/flatbuffers/ https://flatbuffers.dev/flatbuffers_guide_use_python.html https://github.com/google/flatbuffers/blob/master/samples/sample_binary.py
https://flatbuffers.dev/flatbuffers_guide_tutorial.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.12, 2.0, 23.1.4, 23.5.26
Faster: 1.12, 2.0, 23.1.4
flex Aces, Faster, Ookami flex (fast lexical analyzer generator) is a tool for generating scanners: programs which recognize lexical patterns in text.
Description Source: https://github.com/westes/flex
1. Generates C source code for lexical analyzers based on specified patterns.
2. Provides a fast and efficient tool for performing text pattern matching.
3. Offers flexibility in defining scanner descriptions using regular expressions and associated actions.
4. Supports the development of scanners for use in various text processing applications.
Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator https://github.com/westes/flex https://westes.github.io/flex/manual/ http://alumni.cs.ucr.edu/~lgao/teaching/flex.html
https://westes.github.io/flex/manual/Common-Patterns.html#Common-Patterns
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.6.4
Faster: 2.6.3, 2.6.4
Ookami: 2.6.4
Flex is a fast lexical analyzer generator. It is a tool for creating programs that perform pattern-matching on text. It reads the given input files for a description of a scanner to generate and produces a C source file for the scanner. The output file, lex.yy.c, can then be compiled and linked with the flex runtime library to produce an executable. The resulting executable will scan input files for occurrences of the regular expressions in the scanner description, and perform actions specified in the description.
flexiblas Aces, Delta, Faster Library Computational Software Other Mathematics FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
Description Source: https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release
Efficient Implementations Of Blas Routines, Support For Various Hardware Platforms Including Cpus, Gpus, & Accelerators, High Performance Optimization Techniques, Lightweight & Easy To Use Blas Library, Scientific Computing, Linear Algebra https://www.mpi-magdeburg.mpg.de/projects/flexiblas https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release#documentation https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release/-/tree/master/examples?ref_type=heads Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.0.4, 3.2.0, 3.2.1, 3.3.1
Delta: 3.3.0
Faster: 3.0.4, 3.2.0, 3.2.1, 3.3.1
FlexiBLAS is a lightweight BLAS (Basic Linear Algebra Subprograms) library that aims to provide efficient and flexible implementations of BLAS routines for various hardware platforms. It is designed to optimize performance on CPUs, GPUs, and other accelerators, making it suitable for a wide range of scientific computing applications.
flit Aces, Faster Building & Distribution Tool Package Management Tool Computer & Information Sciences A simple packaging tool for simple packages. Building Python Packages, Distributing Python Packages Python Packaging, Package Management Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.9.0
Faster: 3.9.0
Flit is a simple tool for building and distributing Python packages.
fltk Aces, Faster Development Tool Cross-Platform Gui Library Engineering & Technology FLTK is a cross-platform C++ GUI toolkit for UNIX®/Linux® (X11), Microsoft® Windows®, and macOS®. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL® and its built-in GLUT emulation.
Description Source: https://www.fltk.org/
Cross-Platform Gui Development, Multiple Widgets For Building Interfaces, Event Handling & Callback Functionality, Support For Opengl Integration, Lightweight & Fast Performance Gui Toolkit, Cross-Platform Development, C++ Library https://www.fltk.org/ https://fltk.gitlab.io/fltk/ https://fltk.gitlab.io/fltk/basics.html
https://fltk.gitlab.io/fltk/examples.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.3.8
Faster: 1.3.5, 1.3.7, 1.3.8
FLTK (Fast, Light Toolkit) is a cross-platform C++ GUI toolkit for developing graphical user interfaces. It provides various widgets and tools for creating interactive and responsive graphical applications.
flye Anvil Bioinformatics Tool Assembly Biological Sciences Genome Assembly & Analysis Genomics Flye: Fast and accurate de novo assembler for single molecule sequencing reads 1. Long-read assembly 2. Utilizes nanopore sequencing data 3. Accurate genome assemblies 4. High-quality output Genome Assembly, Long-Read Sequencing, Nanopore Sequencing Anvil: https://www.rcac.purdue.edu/software/flye Anvil: 2.9, 2.9.1, 2.9.2 Flye is a long-read assembler designed to assemble genomes using nanopore sequencing data. It aims to provide accurate and high-quality genome assemblies by utilizing long reads.
fms2 Ookami Source-To-Source Compiler Compiler Other Computer & Information Sciences fms2 offers automatic translation of legacy Fortran code to modern C++ for enhanced performance, supports Fortran 77/90/95 standards, assists in porting legacy scientific applications to modern architectures, provides optimizations for improved computational efficiency. Compiler, Software, Translation https://github.com/NOAA-GFDL/FMS https://noaa-gfdl.github.io/FMS/ https://noaa-gfdl.github.io/FMS/autotools.html
https://noaa-gfdl.github.io/FMS/cmake.html
https://noaa-gfdl.github.io/FMS/md_TESTING.html
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: Gcc12.1.0/2022.04 fms2 is an efficient and flexible Fortran to C++ source-to-source compiler that aids in translating Fortran 77/90/95 code to modern C++ code, enabling improved performance and compatibility.
foldseek Faster Library Computational Biology Biological Sciences Bioinformatics Biological Sciences Prediction Of RNA Secondary Structures, Utilizes Deep Learning Models, Specifically Cnns, Python-Based Package, Allows For Training Custom Models RNA Secondary Structure Prediction, Deep Learning Models, Python Package Faster: https://hprc.tamu.edu/software/faster/ Faster: 3-915Ef7D-Linux64-Avx2 FoldSeek is a Python package for predicting RNA secondary structures using deep learning models. It utilizes Convolutional Neural Networks (CNNs) to learn the complex patterns in RNA sequences and predict the secondary structures.
fontconfig Aces, Faster System Tool Library Engineering & Technology Fontconfig is a library for configuring and customizing font access.
Description Source: https://www.freedesktop.org/wiki/Software/fontconfig/
System-Wide Font Configuration, Font Discovery & Access For Applications, Font Aliasing & Subsetting, Font Caching For Performance Optimization Fontconfig, Font Management, Font Configuration, Linux, Unix-Like Systems https://www.freedesktop.org/wiki/Software/fontconfig/ https://fontconfig.pages.freedesktop.org/fontconfig/fontconfig-user.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.13.92, 2.13.93, 2.13.94, 2.14.0, 2.14.1, 2.14.2
Faster: 2.13.1, 2.13.92, 2.13.93, 2.13.94, 2.14.0, 2.14.1, 2.14.2
Fontconfig is a library designed to provide system-wide font configuration, customization, and management for user interfaces and text display on Linux and other Unix-like operating systems. It allows applications to discover and access fonts, and provides settings for font selection, aliasing, subsetting, and caching.
formats Faster Faster: https://hprc.tamu.edu/software/faster/
foss Aces, Faster Software Library Development Tools Other Computer & Information Sciences The foss common compiler toolchain consists entirely of open source software (hence the name, derived from the common term 'FOSS', which is short for "Free and Open Source Software").
Description Source: https://docs.easybuild.io/common-toolchains/#common_toolchains_foss
1. Free for distribution and modification. 2. Access to the source code for transparency and customization. 3. Collaboration and community-driven development. 4. Cost-effective and sustainable solutions. 5. Promotes innovation and knowledge sharing. Free Software, Open Source Software, Software Development https://docs.easybuild.io/common-toolchains/#common_toolchains_foss https://docs.easybuild.io/common-toolchains/#common_toolchains_foss https://docs.easybuild.io/version-specific/toolchain-opts/#foss Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2020B, 2021A, 2021B, 2022A, 2022B, 2023A, 2023B, 2023.09
Faster: 2018B, 2019B, 2020A, 2020B, 2021A, 2021B, 2022A, 2022B, 2023A, 2023B
FOSS (Free and Open Source Software) refers to software that is both free to use and distribute, as well as with access to the source code for modification or enhancement by users.
fosscuda Aces, Faster Compiler/Library Software Development/Tools Computer & Information Sciences Artificial Intelligence & Intelligent Systems Computer Science fosscuda is a compiler toolchain with GCC+CUDA, OpenMPI, OpenBLAS, ScaLAPACK and FFTW.
Description Source: https://docs.easybuild.io/api/easybuild/toolchains/fosscuda/?h=fosscuda
1. Provides open-source alternatives to proprietary CUDA tools. 2. Enables accelerated computing on NVIDIA GPUs. 3. Supports parallel processing and high-performance computing applications. 4. Includes libraries and frameworks for GPU-accelerated programming. Cuda, Gpu Computing, Parallel Programming, Open-Source https://docs.easybuild.io/common-toolchains/#common_toolchains_foss https://docs.easybuild.io/common-toolchains/#common_toolchains_foss https://docs.easybuild.io/version-specific/toolchain-opts/#fosscuda Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2020B
Faster: 2019B, 2020A, 2020B
FOSSCUDA stands for Free and Open-Source Software for CUDA (Compute Unified Device Architecture) and is a collection of tools and libraries that enable developers to leverage the power of NVIDIA GPUs for parallel computing tasks.
fq Anvil Command-Line Tool Bioinformatics Tool Biological Sciences Fq is a command line utility for manipulating Illumina-generated FastQ files. Filtering Fastq Files Based On Quality Scores, Filtering Reads Based On Length, Modifying Read Headers & Sequences, Command-Line Interface For Easy Usage Fastq File Manipulation, High-Throughput Sequencing Data Processing, Biological Sequence Analysis Anvil: https://www.rcac.purdue.edu/software/fq Anvil: 0.10.0 fq is a command-line tool for filtering and manipulating FASTQ files, which are used to store biological sequences and their quality scores obtained from high-throughput sequencing. It provides functionalities for filtering reads based on quality scores, length, and other criteria, as well as for modifying read headers and sequences.
fraggenescan Anvil Bioinformatics Gene Prediction Biological Sciences Genetics Biological Sciences Fraggenescan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. 1. Prediction Of Protein-Coding Sequences, 2. Designed For Short Reads From Ngs Technology, 3. Particularly Useful For Metagenomic & Single-Cell Sequencing Data, 4. Supports Both Metagenomic & Whole Genome Sequencing Data Gene Prediction, Ngs Data Analysis, Metagenomics, Single-Cell Sequencing Anvil: https://www.rcac.purdue.edu/software/fraggenescan Anvil: 1.31 FragGeneScan is a gene-finding program specifically designed for short reads from next-generation sequencing (NGS) technology. It predicts protein-coding sequences in short DNA sequences such as metagenomic and single-cell sequencing data.
fraggenescanrs Anvil Tool Bioinformatics Biological Sciences Bioinformatics Biological Sciences FragGeneScanRs is a better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads. Accurate Gene Prediction In Metagenomic Data, Suitable For Short Reads & Fragmented Assemblies, Improved Performance In Predicting Protein-Coding Genes, Support For Various Input Formats Gene Prediction, Metagenomics, Fragmented Assemblies Anvil: https://www.rcac.purdue.edu/software/fraggenescanrs Anvil: 1.1.0 FragGeneScanRS is a robust tool for gene prediction in metagenomes and fragmented assemblies, specifically designed to accurately predict protein-coding genes in short reads and incomplete assemblies.
freebayes Anvil, Faster Tool Genomic Variant Calling Tool Biological Sciences Genomics Bioinformatics Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. Detection Of Small Polymorphisms Including Snps, Indels, & Complex Events, Designed For Short-Read Sequencing Data, Utilizes A Bayesian Algorithm For Variant Detection Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm Anvil: https://www.rcac.purdue.edu/software/freebayes
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 1.3.5, 1.3.6
Faster: 1.3.4-Linux-Static-Amd64
FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
freeglut Aces, Faster Graphics Library Libraries Computer & Information Sciences freeglut is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library. GLUT (and hence freeglut) takes care of all the system-specific chores required for creating windows, initializing OpenGL contexts, and handling input events, to allow for trully portable OpenGL programs.
Description Source: https://freeglut.sourceforge.net/
Cross-Platform Support, Window Management, User Input Handling, Event-Driven Programming, Opengl Integration Graphics Programming, Opengl, Cross-Platform Development, Free Software https://freeglut.sourceforge.net/ https://freeglut.sourceforge.net/docs/api.php https://github.com/freeglut/freeglut/blob/master/README.cmake Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.2.1, 3.2.2, 3.4.0
Faster: 3.2.1, 3.2.2
FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library. It provides a simple, platform-independent API for creating windows, sub-windows, and menus, as well as handling input from keyboard, mouse, and joystick devices. FreeGLUT aims to be as close to the original GLUT functionality as possible while also improving and extending it.
freeimage Faster Graphics Library Library Engineering & Technology Support For Various Image Formats Including Bmp, Gif, Png, Jpeg, Tiff, & More, Image Loading & Saving Functionality, Image Conversion & Manipulation Tools, High-Quality Image Processing Algorithms, Suitable For Use In Graphics, Digital Photography, Medical Imaging, & Other Applications Graphics Library, Image Processing, Open-Source Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.18.0 FreeImage is an open-source graphics library that supports popular image formats and features image loading, saving, conversion, manipulation, and processing capabilities.
freeipmi Ookami Management & Monitoring Tool Systems Software Computer & Information Sciences FreeIPMI provides in-band and out-of-band IPMI software based on the IPMI v1.5/2.0 specification. The IPMI specification defines a set of interfaces for platform management and is implemented by a number of vendors for system management. The features of IPMI that most users will be interested in are sensor monitoring, system event monitoring, power control, and serial-over-LAN (SOL).
Description Source: https://www.gnu.org/software/freeipmi/
Remote Power Control, Sensor Monitoring, System Event Log Retrieval, Fru Data Retrieval, Health Monitoring Bmc, Baseboard Management Controller, Open-Source, Hardware Management, Monitoring https://www.gnu.org/software/freeipmi/index.html https://www.gnu.org/software/freeipmi/documentation.html https://www.gnu.org/software/freeipmi/README.build
https://www.gnu.org/software/freeipmi/freeipmi-hostrange.txt
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 1.6.4 FreeIPMI is an open-source BMC (Baseboard Management Controller) software that provides a consistent and reliable interface for managing and monitoring IPMI-compliant systems. It allows administrators to remotely manage server hardware, monitor sensors, power on/off servers, and perform other BMC-related functions.
freesurfer Expanse Scientific Imaging Analysis Biological Sciences Neuroimaging Neuroscience Automatic Segmentation Of Brain Mri Data, Cortical Surface Reconstruction, Volume Measurements Of Brain Structures, Functional Mri Analysis Tools, Visualization Of Neuroimaging Data Neuroimaging, Mri Analysis, Brain Segmentation, Functional Mri, Image Visualization Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 7.1.1, 7.2.0 FreeSurfer is a software suite used for the analysis and visualization of structural and functional neuroimaging data from MRI and CT scans. It is widely used in the field of neuroscience and neuroimaging research.
freetype Aces, Faster Font Engine Operating System/Graphic Library Computer & Information Sciences FreeType is a freely available software library to render fonts.
Description Source: https://freetype.org/
1. Support for several font formats including TrueType, OpenType, Type 1, and CID-keyed fonts.
2. Efficient rendering of high-quality glyph images.
3. Ability to hint fonts to improve rendering at small sizes.
4. Comprehensive API for developers to integrate font handling and rendering into their applications.
5. Portable across different platforms such as Windows, macOS, Linux, and more.
Font Engine, Text Rendering, Typography https://freetype.org/ https://freetype.org/freetype2/docs/reference/index.html https://freetype.org/freetype2/docs/tutorial/index.html
https://freetype.org/freetype2/docs/tutorial/step3.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.10.3, 2.10.4, 2.11.0, 2.12.1, 2.13.0
Faster: 2.10.1, 2.10.3, 2.10.4, 2.11.0, 2.12.1, 2.13.0
FreeType is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in various applications that require text rendering, such as operating systems, web browsers, desktop publishing tools, and more.
freexl Aces, Faster Data Extraction Library Computer & Information Sciences FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. 1. Reading data from Excel (.xls) files
2. No dependency on Microsoft Excel
3. Cross-platform compatibility
4. Simple API for easy integration into other projects
Excel, Spreadsheet, Data Extraction Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.6
Faster: 1.0.6
FreeXL is a library to extract data from Excel (.xls) spreadsheet files. The library allows for reading Excel files without the need for Microsoft Excel to be installed.
freyja Anvil Molecular Modeling Computational Software Chemical Sciences Chemical Sciences Physical Sciences Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset. Molecular Dynamics Simulations, Quantum Mechanical Calculations, Energy Minimization, Molecular Structure Optimization, Visualization Of Molecular Systems Computational Chemistry, Quantum Mechanics, Molecular Simulations, Molecular Modeling, Chemistry Software Anvil: https://www.rcac.purdue.edu/software/freyja Anvil: 1.3.11, 1.4.2 Freyja is a software tool designed for computational chemistry and quantum mechanics calculations. It provides a range of functionalities to simulate and analyze molecular systems.
fribidi Aces, Faster, Ookami Text Processing Library Computer & Information Sciences The Free Implementation of the Unicode Bidirectional Algorithm.
Description Source: https://github.com/fribidi/fribidi?tab=readme-ov-file
Implementation Of The Unicode Bidirectional Algorithm, Utility Functions For Working With Bidirectional Text Unicode, Bidirectional Algorithm https://github.com/fribidi/fribidi https://github.com/fribidi/fribidi?tab=readme-ov-file#api https://github.com/fribidi/fribidi/tree/master/test Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 1.0.10, 1.0.12
Faster: 1.0.5, 1.0.9, 1.0.10, 1.0.12
Ookami: 1.0.13
GNU FriBidi is an implementation of the Unicode Bidirectional Algorithm (bidi). It also provides utility functions to help work with bidirectional text.
fseq Anvil Python Library Bioinformatics Biological Sciences Functional Genomics Genomics Fseq is a feature density estimator for high-throughput sequence tags Peak Calling In Chip-Seq & DNAse-Seq Data, Identification Of Enriched Regions In The Genome, Analysis Of Potential Binding Sites Of Proteins Or Functional Elements Genomics, Peak Calling, Functional Genomics, Python Package Anvil: https://www.rcac.purdue.edu/software/fseq Anvil: 2.0.3 F-seq is a Python package that provides tools for peak calling and peak detection in functional genomics datasets, specifically ChIP-seq and DNase-seq data. It is designed to identify enriched regions in the genome that represent potential binding sites of proteins or other functional elements.
fsl Faster Image Processing Software Medical Imaging Software Biological Sciences Biophysics, Neuroscience Biological Sciences Some core features of FSL include preprocessing of MRI data for better analysis, registration of images to a standard space, statistical analysis of MRI data, and tools for brain segmentation and visualization. Mri, Imaging, Neuroimaging, Data Analysis, Image Processing Faster: https://hprc.tamu.edu/software/faster/ Faster: 6.0.5-Slurm FSL (FMRIB Software Library) is a comprehensive library of analysis tools for functional, structural, and diffusion MRI brain imaging data. It provides various image processing tools to process and analyze data acquired using MRI techniques.
ftp Anvil Tool Networking & Communication A File Transfer Protocol client (FTP client) is a software utility that establishes a connection between a host computer and a remote server, typically an FTP server. File Transfer Between Client & Server, Upload & Download Files & Directories, Rename, Delete, & Create Directories, Authentication & Security Features Network Protocol, File Transfer, Client-Server Communication Anvil: https://www.rcac.purdue.edu/software/ftp Anvil: 0.17 FTP (File Transfer Protocol) is a standard network protocol used for the transfer of computer files between a client and server on a computer network. It allows users to upload or download files and directories, as well as perform other file operations such as renaming, deleting, and creating directories.
fujitsu Ookami Computer & Information Sciences Fujitsu provides innovative solutions in the areas of cloud computing, big data analytics, artificial intelligence, IoT, and cybersecurity. Their products and services cater to various industries including finance, healthcare, retail, and manufacturing. It Services, Information Technology, Hardware, Software https://www.fujitsu.com/emeia/products/computing/servers/mainframe/bs2000/software/programming/cpp.html https://software.fujitsu.com/jp/manual/manualindex/p22000026e.html https://www.stonybrook.edu/commcms/ookami/support/faq/ookami-fujitsu-compilers
https://software.fujitsu.com/jp/manual/manualfiles/m200007/j2ul2578/02enz000/j2ul-2578-02enz0.pdf
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Fujitsu is a multinational information technology equipment and services company headquartered in Tokyo, Japan. Fujitsu offers a wide range of products and services including servers, storage systems, software, networking equipment, and more.
funannotate Anvil, Bridges-2 Bioinformatics Tool Genome Annotation Biological Sciences Genetics Biological Sciences Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes.
Description Source: https://funannotate.readthedocs.io/en/latest/#
Automated Genome Prediction & Annotation For Fungi, Gene Model Prediction Using Multiple Tools, Functional Annotation With Interproscan, Signalp, & Other Databases, Comparative Genomics Analysis For Multiple Genomes, User-Friendly Interface For Customization & Visualization Genome Prediction, Genome Annotation, Fungi, Bioinformatics https://github.com/nextgenusfs/funannotate https://funannotate.readthedocs.io/en/latest/ https://funannotate.readthedocs.io/en/latest/tutorials.html Anvil: https://www.rcac.purdue.edu/software/funannotate
Bridges-2: https://www.psc.edu/resources/software/funannotate
Anvil: 1.8.10, 1.8.13
Bridges-2: 1.8.9
funannotate is a pipeline for genome prediction and annotation of fungi. It automates the process of predicting gene models, functional annotation, and comparative genomics analysis for fungal genomes.
futhark Faster Compiler Programming Language Computer & Information Sciences Purely Functional Programming Language, Data-Parallel Programming Model, Designed For Gpu Programming, High-Performance Computing Capabilities Programming Language, Data-Parallel Programming, Gpu Programming, High-Performance Computing Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.19.5 Futhark is a purely functional data-parallel programming language that aims to make high-performance GPU programming approachable to a wider audience. It is designed for efficiently running complex computations on modern GPUs.
fwdpy11 Anvil Python Library Simulation Tool Biological Sciences Population Genetics Biological Sciences Fwdpy11 is a Python package for forward-time population genetic simulation. Simulation Of Genetic Drift, Forward-Time Population Genetics Modeling, Genetic Data Analysis Tools, Support For Various Evolutionary Scenarios, Efficient & Flexible Simulation Capabilities Population Genetics, Genetic Simulation, Python Library, Genetic Data Analysis Anvil: https://www.rcac.purdue.edu/software/fwdpy11 Anvil: 0.18.1 fwdpy11 is a flexible and efficient Python library for forward-time population genetics simulations. It provides tools for simulating a wide range of evolutionary scenarios and analyzing the resulting genetic data.
g2clib Aces, Faster Computational Tool Library Earth & Environmental Sciences Library contains GRIB2 encoder/decoder ('C' version). 1. Reading and writing GEMPAK files
2. Geophysical data manipulation
3. Support for meteorological data
4. Data analysis and visualization functions
Geophysics, Meteorology, Data Manipulation, Data Analysis Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.6.3
Faster: 1.6.0
g2clib is a library for the manipulation of geophysical data in the GEMPAK format. It provides routines for reading, writing, and manipulating meteorological and geophysical data.
g2lib Aces Computational Software Library Computer & Information Sciences Library contains GRIB2 encoder/decoder and search/indexing routines. 1. Robust geometric algorithms for intersection testing, distance computation, convex hulls, triangulation, Voronoi diagrams, etc.
2. Support for both 2D and 3D geometric operations.
3. Implementation of algorithms like line-line intersection, point location, closest point on a segment, and more.
4. Suitable for applications in computer graphics, visualization, spatial analysis, and geometric modeling.
Computational Geometry, Computer Graphics, Geometric Computing Aces: https://hprc.tamu.edu/software/aces/ Aces: 3.2.0 g2lib is a C++ library for 2D and 3D geometric computing, mainly focusing on computational geometry and computer graphics. It provides efficient and robust geometric algorithms for various tasks.
gadma Anvil Tool Bioinformatics Biological Sciences Genetics Biological Sciences GADMA is a command-line tool. Basic pipeline presents a series of launches of the genetic algorithm folowed by local search optimization and infers demographic history from the Allele Frequency Spectrum of multiple populations. 1. Utilizes genetic algorithm techniques for identifying mutually exclusive alterations. 2. Provides visualization tools for results interpretation. 3. Supports input data from various cancer genomics studies. 4. Allows customization of parameters to refine analysis. 5. Facilitates the discovery of potential driver genes in cancer. Genetic Algorithm, Cancer Genomics, Mutually Exclusive Alterations, Driver Genes Anvil: https://www.rcac.purdue.edu/software/gadma Anvil: 2.0.0Rc21 GADMA (Genetic Algorithm for Detecting Mutually exclusive Alterations) is a tool for identifying mutually exclusive alterations in cancer using a genetic algorithm approach.
gambit Anvil Software Package Computational Game Theory Tool Social Sciences Game Theory Economics & Business GAMBIT (Genomic Approximation Method for Bacterial Identification and Tracking) is a tool for rapid taxonomic identification of microbial pathogens. 1. Representation of games in extensive and strategic form
2. Computation of Nash equilibria and other solution concepts
3. Analysis of strategic interaction and decision-making
4. Visualization of game theoretic solutions
5. Support for various game types and player settings
Game Theory, Computational Analysis, Nash Equilibria Anvil: https://www.rcac.purdue.edu/software/gambit Anvil: 0.5.0
Ookami: 4.9.5
Gambit is an open-source software package for carrying out computational game theory analysis. It provides tools for the representation, numerical solution, and strategic analysis of games, including extensive support for the computation of Nash equilibria.
gamess Bridges-2, Expanse Quantum Chemistry Computational Software Chemical Sciences Chemical Sciences Physical Sciences GAMESS (General Atomic and Molecular Electronic Structure System) is used for ab initio quantum chemistry calculations. It provides a wide range of methods for studying molecular systems, including ground state energies, molecular geometry optimization, and electronic properties, making it a valuable tool for researchers in chemistry and physics. GAMESS offers an extensive variety of quantum chemistry methods, including Hartree-Fock, density functional theory (DFT), Moller-Plesset perturbation theory, configuration interaction, coupled cluster, and more. It also supports a variety of basis sets, including Gaussian basis functions and Slater-type basis sets. GAMESS is highly configurable and enables users to perform geometry optimizations, vibrational frequency calculations, transition state searches, and other advanced electronic structure calculations. Quantum Chemistry, Electronic Structure Calculations, Ab Initio Calculations https://www.msg.chem.iastate.edu/gamess/index.html https://www.msg.chem.iastate.edu/gamess/documentation.html https://www.msg.chem.iastate.edu/tutorials/tutorials.html Bridges-2: https://www.psc.edu/resources/software/gamess
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Bridges-2: 2020
Expanse: Eo5Efva
Stampede-3: 2023.06.30
The General Atomic and Molecular Electronic Structure System (GAMESS) is a suite of ab initio quantum chemistry programs designed for electronic structure calculations of molecules and molecular reactions. It provides a wide range of methods for both molecules and periodic solids.
gamma Anvil Library Computational Software Mathematics Statistics & Probability GAMMA (Gene Allele Mutation Microbial Assessment) is a command line tool that finds gene matches in microbial genomic data using protein coding (rather than nucleotide) identity, and then translates and annotates the match by providing the type (i.e., mutant, truncation, etc.) 1. Probabilistic modeling
2. Bayesian inference
3. Statistical analysis
4. Parameter estimation
5. Uncertainty quantification
Probabilistic Modeling, Bayesian Inference, Statistical Analysis Anvil: https://www.rcac.purdue.edu/software/gamma Anvil: 1.4, 2.2 Gamma is a software package for probabilistic modeling, Bayesian inference, and statistical analysis. It provides tools for fitting complex models to data, performing parameter estimation, and uncertainty quantification.
gangstr Anvil Genomic Analysis Tool Bioinformatics Tool Biological Sciences Population Genetics Genomics GangSTR is a tool for genome-wide profiling tandem repeats from short reads. 1. Genotyping and discovery of short tandem repeats (STRs) from sequencing data
2. Optimized for whole-genome sequencing data
3. Designed for population-scale studies
4. Accurate detection of STR variation
Str, Genotyping, Short Tandem Repeats, Sequencing Data Analysis Anvil: https://www.rcac.purdue.edu/software/gangstr Anvil: 2.5.0 GangSTR is a tool for profiling short tandem repeats (STRs) from high-throughput sequencing data. It is specifically designed for examining STR variation in whole-genome sequencing data and is optimized for population-scale studies, allowing for accurate STR genotyping and discovery.
gapfiller Anvil Computational Tool Genome Assembly Biological Sciences Genomics Bioinformatics GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. Utilizes Paired-End Reads For Gap Filling, Improves Genome Assembly Accuracy, Enhances Assembly Completeness, Provides Detailed Elucidation Of Sequencing Gaps Genome Assembly, Bioinformatics, Sequencing, Gap Filling Anvil: https://www.rcac.purdue.edu/software/gapfiller Anvil: 2.1.2 GapFiller is a software tool designed for closing gaps and improving genome assemblies by utilizing paired-end reads. It works by enabling the precise elucidation of gaps that occur during the sequencing and assembly process, ultimately enhancing the accuracy and completeness of the assembled genome.
gapit Anvil Tool Bioinformatics Agricultural Sciences Crop Genetics Agricultural Sciences GAPIT is a Genome Association and Prediction Integrated Tool. Conduct Genome-Wide Association Studies (Gwas), Perform Genomic Prediction, Supports A Variety Of Statistical Models, Data Visualization Tools, User-Friendly Interface Gwas, Genomic Prediction, Crop Genetics Anvil: https://www.rcac.purdue.edu/software/gapit Anvil: 3.3 GAPIT (Genome Association and Prediction Integrated Tool) is a comprehensive software package developed for genome-wide association studies (GWAS) and genomic prediction in crops. It provides a user-friendly interface to perform various statistical analyses and data visualization related to genetic studies in plants.
gatk Aces, Anvil, Bridges-2, Expanse, Faster Tool Bioinformatics Tool Biological Sciences Sciences Biology GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery. The tools can be used individually or chained together into complete workflows.
Description Source: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4
Core features of GATK include variant discovery, genotyping, recalibration of base quality scores, read alignment improvement, variant annotation, and various filtering and preprocessing steps. It supports a wide range of variant calling methodologies and has modules for germline and somatic variant detection. Variant Calling, Genotyping, Sequencing Analysis https://gatk.broadinstitute.org/hc/en-us https://gatk.broadinstitute.org/hc/en-us/articles/21904996835867--Tool-Documentation-Index https://gatk.broadinstitute.org/hc/en-us/sections/360007226631-Tutorials Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gatk
Bridges-2: https://www.psc.edu/resources/software/gatk
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.4.0.0-Java-17
Anvil: 3.8, 4.1.8.1
Bridges-2: 4.1.9.0
Expanse: Ybsfk6K
Faster: 4.2.0.0-Java-1.8, 4.2.5.0-Java-11
The Genome Analysis Toolkit (GATK) is a widely used software package for variant discovery and genotyping analysis in high-throughput sequencing data. Developed by the Broad Institute, GATK provides a robust and comprehensive set of tools for processing raw sequencing data into accurate variant calls.
gatk4 Anvil Genomic Analysis Tool Data Analysis Biological Sciences Genomics Biological Sciences GATK (Genome Analysis Toolkit) is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discoverye. 1. Variant discovery and genotyping
2. Joint variant calling in cohorts
3. Quality control and variant filtration
4. Haplotype phasing and imputation
5. Structural variant discovery
6. Functional annotation of variants
Bioinformatics, Genomic Analysis, Variant Discovery, High-Throughput Sequencing Anvil: https://www.rcac.purdue.edu/software/gatk4 Anvil: 4.2.0, 4.2.5.0, 4.2.6.1, 4.3.0.0 The Genome Analysis Toolkit (GATK) is a software package developed at the Broad Institute to analyze high-throughput sequencing data. The toolkit offers a wide variety of tools for variant discovery, genotyping, and other genomic analyses.
gaussian Bridges-2, Darwin, Expanse, Faster Simulation Software Scientific Software Natural Sciences Physical Chemistry Chemical Sciences Gaussian is a computational chemistry software for quantum mechanical simulations, widely used by researchers for studying molecular structures and reactions. It offers advanced capabilities in electronic structure prediction and various spectroscopic properties analysis. Key features of Gaussian include ab initio and density functional theory calculations, molecular dynamics simulations, electronic and vibrational spectroscopy, reaction mechanism analysis, and transition state optimization. It supports a wide range of methods and basis sets for accurate quantum chemical calculations. Computational Chemistry, Quantum Chemistry, Molecular Modeling https://gaussian.com/ https://gaussian.com/man/ https://gaussian.com/faq/
https://www.youtube.com/GaussianInc
Bridges-2: https://www.psc.edu/resources/software/gaussian
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Bridges-2: G16_Revc01
Expanse: 16.C.01-Cuda, 16.C.01
Faster: G16_B01, G16_C01
Stampede-3: 16Rc.01
Gaussian is a computational chemistry software suite used for electronic structure modeling. It is widely utilized in research and industry for predicting molecular properties and simulating chemical processes.
gaussian09 Expanse Computational Software Quantum Chemistry Software Chemical Sciences Physical Chemistry 1. Perform ab initio and DFT calculations for molecules and reactions.
2. Predict electronic and molecular structures, energies, and spectra.
3. Explore potential energy surfaces and reaction mechanisms.
4. Study molecular properties like dipole moments, polarizabilities, and vibrational frequencies.
Quantum Chemistry, Quantum Mechanics, Molecular Modeling Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 09.D.01, 09.E.01 Gaussian09 is a software suite for quantum chemistry calculations, widely used for predicting molecular properties and behaviors based on quantum mechanics principles.
gawk Faster, Kyric Text Processing Tool Command-Line Utility Computer & Information Sciences Sciences Chemistry GaussView aids in the creation of Gaussian input files, enables the user to run Gaussian calculations from a graphical interface without the need for using a command line instruction, and helps in the interpretation of Gaussian output.
Description Source: https://gaussian.com/gaussview6/
1. Pattern scanning and processing of text files
2. Automatic data restructuring and report generation
3. Advanced text manipulation capabilities
4. User-defined functions and variables
5. Conditional control structures for data processing
Text Processing, Data Manipulation, Pattern Scanning https://gaussian.com/gaussview6/ https://gaussian.com/wp-content/uploads/dl/gv6.pdf https://gaussian.com/gv6main/ Faster: https://hprc.tamu.edu/software/faster/ Faster: 5.0.1, 5.1.1 Gawk is a powerful text processing utility that allows for pattern scanning and processing. It is based on the Awk programming language and is particularly useful for manipulating text files and generating reports.
gc Aces, Faster Programming Language Compiler Compiler Computer & Information Sciences, Computer Science Software Engineering, Systems, & Development Computer Science The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. GC provides garbage collection, concurrency support, memory safety, and a standard library. Compiler, Go, Garbage Collection, Concurrency Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.2.0, 8.2.4
Faster: 7.6.12, 8.2.0, 8.2.4
GC is a compiler for the Go programming language.
gcatools Faster Tool Analysis Tool Biological Sciences Genomics Bioinformatics Quality Control Of Sequencing Data, Alignment Of Sequencing Reads To A Reference Genome, Identification Of Genetic Variants, Annotation Of Genomic Sequences Genomic Data Analysis, Next-Generation Sequencing, Bioinformatics Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.0 gcatools is a set of tools designed to analyze and process genomic data generated from next-generation sequencing experiments. It offers a variety of functionalities for quality control, alignment, variant calling, and annotation of genomic sequences.
gcc Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Kyric, Ookami, Stampede3 Development Tools Compiler Computer Science GCC, the GNU Compiler Collection, is an open-source compiler system that supports various programming languages like C, C++, Objective-C, Fortran, Ada, and Go. It is widely used in software development for compiling source code into executable programs, providing robust performance and extensive compatibility across different platforms and operating systems.
Description Source: https://gcc.gnu.org/
1. Supports multiple programming languages such as C, C++, Fortran, Ada, and Objective-C.
2. Optimizes code for better performance with various optimization levels.
3. Generates executable code for different target architectures.
4. Includes preprocessor for handling macro definitions and conditional compilation.
5. Provides extensive error and warning messages for code analysis.
6. Supports various platforms including Linux, Windows, macOS, and BSD.
Compiler, Software Development, Programming https://gcc.gnu.org/ https://gcc.gnu.org/onlinedocs/gcc-13.2.0/gcc/ https://gcc.gnu.org/wiki/GettingStarted
https://gcc-newbies-guide.readthedocs.io/en/latest/
https://www.geeksforgeeks.org/gcc-command-in-linux-with-examples/
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gcc
Bridges-2: https://www.psc.edu/resources/software/gcc
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 8.3.0, 10.2.0, 10.3.0, 11.2.0, 11.3.0, 12.2.0, 12.3.0, 13.1.0, 13.2.0
Anvil: 8.4.1, 11.2.0-Openacc, 11.2.0
Bridges-2: 10.2.0, 13.2.1-P20240113
Delta: 11.4.0
Expanse: Xiuwkua
Faster: 7.3.0-2.30, 8.3.0, 9.3.0, 10.2.0, 10.3.0, 11.2.0, 11.3.0, 12.1.0, 12.2.0, 12.3.0, 13.1.0, 13.2.0
Ookami: 9.4.0
Stampede-3: 13.2.0
GNU Compiler Collection (GCC) is a free and open-source compiler system that supports various programming languages and platforms. It is widely used for compiling high-level programming languages into executable code for a variety of computer architectures.
gcc-native Delta Native Compiler Compiler Computer & Information Sciences Software Development Computer Science gcc-native provides compilers for various programming languages including C, C++, and Fortran. It supports optimization flags for performance tuning. The system includes a preprocessor, compiler, assembler, and linker. Compiler, Gnu, Programming Language Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 10.3, 11.2 gcc-native is a compiler system produced by the GNU Project supporting various programming languages, most notably C, C++, and Fortran. It is the default compiler for many Unix-like operating systems.
gcc-native-mixed Delta Development Tool Compiler Computer Science Supports mixed-language programming, Optimized for combining multiple programming languages, High performance and efficiency, Comprehensive set of optimization flags, Advanced debugging capabilities Compiler, Mixed-Language Programming, Optimization Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 10.3, 11.2 The gcc-native-mixed compiler is a version of the GNU Compiler Collection (GCC) that is specifically optimized for mixed-language programming, allowing developers to combine different programming languages within the same codebase.
gcc-nvptx Expanse Programming Tool Compiler Computer & Information Sciences Systems & Development Computer Science Generating Ptx Code For Nvidia Gpus, Compiling & Optimizing C & C++ Code For Gpu Execution Compiler, Gpu Programming Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 11.3.1 The Nvidia PTX (Parallel Thread Execution) backend for GCC enables the generation of PTX code, which is a low-level parallel thread execution virtual machine and instruction set architecture used by Nvidia GPUs. It allows users to compile and optimize C and C++ code for Nvidia GPUs.
gcc-runtime Delta Runtime Library Compiler Engineering & Technology Software Development Software Engineering, Systems, & Development 1. Includes runtime libraries needed for programs compiled with GCC. 2. Provides support files required for programs to run correctly. 3. Ensures compatibility and execution efficiency for programs compiled using GCC. Compiler, Runtime, Library Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 8.5.0, 11.4.0 The GCC Runtime Library is a part of the GCC compiler collection that provides runtime support for programs compiled with GCC. It includes various runtime libraries and support files necessary for programs compiled with GCC to execute correctly.
gcccore Aces, Faster Core Component Compiler Computer & Information Sciences, Software Engineering, Systems, & Development The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Ada, Go, and D, as well as libraries for these languages (libstdc++,...). GCC was originally written as the compiler for the GNU operating system.
Description Source: https://gcc.gnu.org/
Key features of gcccore include optimizing compilers for various programming languages such as C, C++, and Fortran, support for multiple architectures and operating systems, advanced optimization techniques, and extensive error-checking capabilities. Compiler, Programming, Software Development https://gcc.gnu.org/ https://gcc.gnu.org/onlinedocs/gcc-13.2.0/gcc/ https://gcc.gnu.org/wiki/GettingStarted
https://gcc-newbies-guide.readthedocs.io/en/latest/
https://www.geeksforgeeks.org/gcc-command-in-linux-with-examples/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.3.0, 10.2.0, 10.3.0, 11.2.0, 11.3.0, 12.2.0, 12.3.0, 13.1.0, 13.2.0
Faster: 7.3.0, 8.2.0, 8.3.0, 9.2.0, 9.3.0, 10.2.0, 10.3.0, 11.2.0, 11.3.0, 12.1.0, ...
gcccore refers to the core components of the GNU Compiler Collection (GCC), which is a collection of compilers for several programming languages. These core components provide essential functionality for compiling code and generating executable programs.
gcccuda Aces, Faster Development Tool Compiler Computer & Information Sciences Parallel & Distributed Computing Computer Science GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. Enables Cuda Programming In C Using Gcc Compiler, No Need For Nvcc, Supports Cuda Features & Optimizations Cuda Programming, C Compiler Wrapper, Parallel Computing https://gcc.gnu.org/ https://gcc.gnu.org/onlinedocs/gcc-13.2.0/gcc/ https://gcc.gnu.org/wiki/GettingStarted
https://gcc-newbies-guide.readthedocs.io/en/latest/
https://www.geeksforgeeks.org/gcc-command-in-linux-with-examples/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2020B
Faster: 2019B, 2020A, 2020B
gcccuda is a wrapper around the GCC C compiler that enables CUDA programming directly in C without the need for NVCC. It allows developers to write CUDA code using familiar C syntax and compile it with the GCC compiler.
gconf Aces, Faster Configuration Management System System Software Computer & Information Sciences GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. Centralized Configuration Database System, Used By Gnome Desktop Environment & Gnome Applications, Stores Settings & Preferences, Provides An Easy Way For Applications To Access & Update Configuration Data Configuration Management, Settings, Preferences, Desktop Environment Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.2.6
Faster: 3.2.6
GConf is a configuration database system used by GNOME desktop environment and other GNOME software applications to store settings and preferences. It provides a centralized location for storing configuration data, allowing applications to access and update settings easily.
gdal Aces, Anvil, Darwin, Expanse, Faster Library Geospatial Data Processing Earth & Environmental Sciences, Engineering & Technology GDAL is a translator library for raster and vector geospatial data formats that is released under an MIT style Open Source License by the Open Source Geospatial Foundation.
Description Source: https://gdal.org/
Supports A Wide Range Of Raster & Vector Geospatial Data Formats, Ability To Translate Between Different Formats, Geospatial Data Manipulation Capabilities, Source, Coordinate System, & Reprojection Support, Can Be Used For Data Conversions, Processing, Analysis, & Visualization Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis https://gdal.org/ https://gdal.org/user/index.html https://gdal.org/tutorials/index.html
https://pcjericks.github.io/py-gdalogr-cookbook/
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gdal
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.2.1, 3.3.0, 3.3.2, 3.5.0, 3.6.2, 3.7.1
Anvil: 2.4.4, 3.2.0
Expanse: Myvhqxy
Faster: 3.0.4-Python-3.8.2, 3.2.1, 3.3.0, 3.3.2, 3.5.0, 3.6.2, 3.7.1
GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats that is released under an X/MIT style Open Source license. It is a collection of geospatial data manipulation libraries that support raster and vector data formats, and includes protocols to access geospatial data sources.
gdb Aces, Anvil, Darwin, Expanse, Faster, Ookami Debugger Software Development Tools Computer & Information Sciences GDB, the GNU Project debugger, allows you to see what is going on `inside' another program while it executes -- or what another program was doing at the moment it crashed.
Description Source: https://sourceware.org/gdb
1. Source-level debugging: Supports multiple languages and allows debugging programs written in C, C++, Ada, Fortran, Go, and more.
2. Breakpoint management: Set breakpoints to pause the program execution at a specified point for inspection.
3. Watchpoints and catchpoints: Monitor and halt program execution when certain memory locations are accessed or when specific exception conditions occur.
4. Call stack and variables: View and manipulate the call stack, examine variables, and evaluate expressions.
5. Reverse debugging: Allows stepping backward through program execution to understand the causes of unexpected behavior.
Debugger, Programming, Software Development https://www.sourceware.org/gdb/ https://sourceware.org/gdb/current/onlinedocs/gdb.html/ https://sourceware.org/gdb/current/onlinedocs/gdb.html/Sample-Session.html#Sample-Session
https://sourceware.org/gdb/wiki/
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gdb
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 13.2
Anvil: 11.1
Expanse: Am633Ff, Vcxzknn, Xs4Oifw
Faster: 13.2
Ookami: 11.1
GDB, the GNU Project debugger, allows you to see what is going on 'inside' another program while it executes or what another program was doing at the moment it crashed.
gdb4hpc Delta Plugin Debugging Tools Engineering & Technology Software Engineering, Systems, & Development Computer Science Some core features of gdb4hpc include advanced debugging capabilities for parallel and distributed applications, support for various HPC programming models such as MPI and OpenMP, improved performance analysis tools, integration with common HPC development environments, and enhanced visualization of parallel program execution. Debugging, Hpc, Parallel Programming, Performance Analysis Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 4.15.1 gdb4hpc is a plugin designed to enhance the GNU Debugger (GDB) for High Performance Computing (HPC) applications. It provides additional features to aid in debugging parallel and distributed applications typically used in HPC environments.
gdbm Faster, Kyric Library Data Management & Storage Computer & Information Sciences Supports Key/Value Pairs, Provides Persistent Storage, Allows Fast Lookup & Retrieval Operations, Enables Efficient Insertion & Deletion Of Data, Offers Api For Database Management Database Management, Key-Value Store, Persistent Storage, Api https://www.gnu.org.ua/software/gdbm/ https://www.gnu.org.ua/software/gdbm/manual/index.html https://www.gnu.org.ua/software/gdbm/manual/Intro.html Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.18.1 GNU dbm (GDBM) is a library that provides an abstraction for a simple database manager. It allows for the creation and manipulation of key/value pairs in a persistent database, with support for fast lookup, retrieval, insertion, and deletion operations.
gdk-pixbuf Aces, Faster Image Processing Library Computer & Information Sciences The Gdk Pixbuf package is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
Description Source: https://www.linuxfromscratch.org/blfs/view/11.2/x/gdk-pixbuf.html
1. Image loading and saving capabilities.
2. Image scaling and transformations.
3. Image compositing.
4. Support for various image formats.
Image Processing, Graphics, Library https://gitlab.gnome.org/GNOME/gdk-pixbuf https://docs.gtk.org/gdk-pixbuf/ https://docs.gtk.org/gdk-pixbuf/class.Pixbuf.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.42.6, 2.42.8, 2.42.10
Faster: 2.38.2, 2.40.0, 2.42.0, 2.42.6, 2.42.8, 2.42.10
The GdkPixbuf library provides a way to load images into a program and manipulate those images. It is used by GTK and GNOME applications to handle images. GdkPixbuf supports loading, saving, scaling, compositing, and transforming images, allowing various graphical operations to be performed on the images.
gdrcopy Aces, Delta, Faster Memory Management Library Computer & Information Sciences Parallel Computing Computer Science GDRCopy is a low-latency GPU memory copy library based on GPUDirect RDMA technology that allows the CPU to directly map and access GPU memory. GDRCopy also provides optimized copy APIs and is widely used in high-performance communication runtimes like UCX, OpenMPI, MVAPICH, and NVSHMEM.
Description Source: https://developer.nvidia.com/gdrcopy
1. CUDA accelerated GPU memory copy operations
2. Support for asynchronous memory copies
3. Efficient data transfer between host and device memory
4. Optimization for different data types
5. Compatible with NVIDIA GPUs
Gpu Memory Copy, Cuda Acceleration, Asynchronous Memory Copies https://developer.nvidia.com/gdrcopy https://github.com/NVIDIA/gdrcopy https://github.com/NVIDIA/gdrcopy?tab=readme-ov-file#tests Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.1-Cuda-11.1.1, 2.2, 2.3, 2.3.1, 2.4
Delta: 2.3
Faster: 2.1-Cuda-11.0.2, 2.1-Cuda-11.1.1, 2.2, 2.3, 2.3.1
gdrcopy is a CUDA accelerated GPU memory copy library for NVIDIA GPUs. It provides efficient memory copy operations between host and device memory with the use of asynchronous memory copies and supports different data types for optimal performance.
geant4 Aces Toolkit Simulation Software Physical Sciences High Energy Physics Particle Physics Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. Monte Carlo Simulation Of Particle Transport Through Matter, Modular Design With A Wide Range Of Physics Processes & Geometries, User-Friendly Interfaces & Visualization Tools, Open-Source & Actively Maintained By A Large International Collaboration Software, Physics, Simulation, Particle Transport Aces: https://hprc.tamu.edu/software/aces/ Aces: 11.1.2 GEANT4 is a toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics, and radiation protection.
geant4-data Aces Datasets for Geant4. Aces: https://hprc.tamu.edu/software/aces/ Aces: 11.1
gemma Anvil Genetic Analysis Bioinformatics Biological Sciences Gemma is a software toolkit for fast application of linear mixed models (LMMs) and related models to genome-wide association studies (GWAS) and other large-scale data sets. 1. Genome-wide association analysis
2. Mixed model framework
3. Efficient handling of large-scale genotype data
4. Wide range of genetic analysis capabilities
Genome-Wide Association Analysis, Genetic Analysis, Mixed Model Framework Anvil: https://www.rcac.purdue.edu/software/gemma Anvil: 0.98.3 Gemma is a software package for genome-wide association analysis in a mixed model framework. It can efficiently handle large-scale genotype data for a wide range of genetic analysis.
gemoma Anvil Genome Mapping Tool Bioinformatics Tool Biological Sciences Computational Biology Bioinformatics Gene Model Mapper (GeMoMa) is a homology-based gene prediction program. GEMoma utilizes a fast and memory-efficient seed-and-extend algorithm to map RNA-Seq reads effectively. It supports various parameters customization for mapping precision. The tool also provides visualization options for mapped reads and gene expression levels. RNA-Seq, Genome Mapping, Gene Expression, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/gemoma Anvil: 1.7.1 GEMoma (Gene Mapper for RNA-Seq Data) is a tool designed for rapid and accurate mapping of RNA-Seq data to a reference genome.
genemark Anvil Algorithm Gene Prediction Biological Sciences Genomics Bioinformatics GeneMark-ES/ET/EP is package including GeneMark-ES, GeneMark-ET and GeneMark-EP+ algorithms. 1. Prediction of protein-coding genes in prokaryotic and eukaryotic genomes.
2. Utilizes advanced algorithms for accurate gene prediction.
3. Provides annotations for predicted genes.
Gene Prediction, Prokaryotic Genomes, Eukaryotic Genomes Anvil: https://www.rcac.purdue.edu/software/genemark Anvil: 4.68, 4.69 GeneMark is a gene prediction software for prokaryotic and eukaryotic genomes. It uses state-of-the-art algorithms to accurately identify protein-coding genes.
genemark-es Bridges-2 Gene Prediction Software Bioinformatics Tool Biological Sciences Genetics Biological Sciences Novel eukaryotic genomes can be analyzed by the self-training GeneMark-ES.
Description Source: http://exon.gatech.edu/GeneMark/
Accurate Prediction Of Protein-Coding Genes In Eukaryotic Genomes, Unsupervised Ab Initio Gene Prediction Approach, Hidden Markov Model Algorithms Gene Prediction, Bioinformatics, Eukaryotic Genomes, Hidden Markov Model http://exon.gatech.edu/GeneMark/ https://github.com/gatech-genemark/GeneMark-E-Docs/tree/main/docs https://github.com/gatech-genemark/GeneMark-E-Docs/blob/main/docs/usage/general.md
https://github.com/gatech-genemark/GeneMark-E-Docs/tree/main/docs/examples
Bridges-2: https://www.psc.edu/resources/software/genemark-es Bridges-2: 4.65 GeneMark-ES (Eukaryotic) is a eukaryotic gene prediction software that accurately predicts the location and structure of protein-coding genes in eukaryotic genomes. It is based on an unsupervised ab initio approach using hidden Markov model algorithms.
genemarks-2 Anvil Prokaryotic Gene Prediction Genome Annotation Gene Annotation Genomics GeneMarkS-2 combines GeneMark.hmm (prokaryotic) and GeneMark (prokaryotic) with a self-training procedure that determines parameters of the models of both GeneMark.hmm and GeneMark. Gene Prediction In Prokaryotic Genomes, Self-Training Algorithm, Identification Of Protein-Coding Genes, Ribosomal RNA Genes, & Trna Genes, Utilizes Hidden Markov Models Gene Prediction, Prokaryotic Genomes, Hidden Markov Models Anvil: https://www.rcac.purdue.edu/software/genemarks-2 Anvil: 1.14_1.25 GeneMarkS-2 is a gene prediction software that utilizes a self-training algorithm to predict genes in prokaryotic genomes. It identifies protein-coding genes, ribosomal RNA genes, and tRNA genes based on hidden Markov models.
generativemodels Aces Project MONAI is a set of open-source, freely available collaborative frameworks built for accelerating research and clinical collaboration in Medical Imaging. The goal is to accelerate the pace of innovation and clinical translation by building a robust software framework that benefits nearly every level of medical imaging, deep learning research, and deployment. Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.2.1-Cuda-11.7.0
genmap Anvil Genetic Mapping Software Bioinformatics Tool Biological Sciences GenMap: Ultra-fast Computation of Genome Mappability. 1. Genetic mapping for linkage analysis
2. Analysis of inheritance patterns of genetic markers
3. Mapping genetic loci to chromosomal regions
4. Family-based genetic studies support
5. Visualization of linkage results
Genetic Mapping, Linkage Analysis, Genetic Loci Mapping, Family-Based Studies Anvil: https://www.rcac.purdue.edu/software/genmap Anvil: 1.3.0 GenMap is a software tool designed for genetic mapping studies, particularly in the context of linkage analysis. It is used to map genetic loci to specific regions of chromosomes by analyzing the inheritance patterns of genetic markers within families.
genomedata Anvil Data Processing Library Biological Sciences Genomics Biological Sciences Genomedata is a format for efficient storage of multiple tracks of numeric data anchored to a genome. Efficient Access To Genome Data & Annotations, Structured & Standardized Handling Of Genomic Data, Data Manipulation, Analysis, & Visualization Capabilities, Integration With Popular Python Libraries For Genomics Genomics, Python Package, Data Analysis, Data Visualization Anvil: https://www.rcac.purdue.edu/software/genomedata Anvil: 1.5.0 genomedata is a Python package that provides efficient and convenient access to genome data and annotations. It allows users to work with genomic data in a structured and standardized manner, enabling easy manipulation, analysis, and visualization of genomics data.
genomepy Anvil Python Library Data Management Biological Sciences Bioinformatics Genomics Genomepy is designed to provide a simple and straightforward way to download and use genomic data. Automatic Download Of Reference Genomes, Support For Multiple Genome Sources Such As Ncbi, Ensembl, Ucsc, Integration With Popular Bioinformatics Tools, Ability To Update & Manage Local Genome Databases Genomics, Bioinformatics, Python, Reference Genomes, Sequence Analysis Anvil: https://www.rcac.purdue.edu/software/genomepy Anvil: 0.12.0, 0.14.0 Genomepy is a Python package for downloading reference genomes and associated annotation files from various sources. It simplifies the process of obtaining genomic data required for bioinformatics analysis.
genomescope2 Anvil Bioinformatics Tool Genome Analysis Tool Biological Sciences Genome Characterization Genomics Genomescope2: Reference-free profiling of polyploid genomes - Heterozygosity estimation
- Repeat content estimation
- Genome size estimation
- K-mer analysis
Genome Analysis, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/genomescope2 Anvil: 2.0 GenomeScope 2 is a software tool for estimating genome characteristics such as heterozygosity, repeat content, and genome size from high-throughput sequencing reads using a k-mer based approach.
genomicconsensus Anvil Bioinformatics Tool Genome Analysis Biological Sciences Sequence Analysis Genomics Genomicconsensus is the current PacBio consensus and variant calling suite. Refining Consensus Sequence Calls, Optimizing Error Correction, Focused On Long & Error-Prone Tgs Platforms, Integration With Bioinformatics Workflows Bioinformatics, Genomics, Sequence Analysis, Error Correction Anvil: https://www.rcac.purdue.edu/software/genomicconsensus Anvil: 2.3.3 GenomicConsensus is a tool for refining consensus sequence calls produced by bioinformatics applications, primarily focusing on long and error-prone Third Generation Sequencing (TGS) platforms such as PacBio Single Molecule, Real-Time (SMRT) sequencing.
genrich Anvil Tool Bioinformatics Biological Sciences Chromatin Biology Genomics & Bioinformatics Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment. Identification Of Enriched Regions In Chip-Seq Data, Statistical Analysis For Significance Assessment, Integration With Genomic Coordinates & Sequence Data, Visualization Of Results For Interpretation Chip-Seq Analysis, Enriched Regions Identification, Bioinformatics Tool Anvil: https://www.rcac.purdue.edu/software/genrich Anvil: 0.6.1 Genrich is a tool designed for analyzing ChIP-seq data, specifically focused on identifying significant regions of enrichment in datasets.
gent Bridges-2 Bioinformatics Tool Computational Tool Biological Sciences Genomics Bioinformatics GeNT is a FORTRAN program that computes the cross entropy for groups of sequences that have been assigned to groups on the basis of biochemical,physiological, or other biological property. The sequence assignments are cross-validated, again by the cross entropy measure, to check for problems with the alignment or group assignment. Sequences that were initially identified as “unclassified” are compared to all of the groups using position specific log-odds scores as described by Henikoff and Henikoff. Positions in the aligned sequences that are important for determining group membership are identified by having a high entropy for the entire alignment and a high entropy for one or more specific groups.
Description Source: https://www.psc.edu/resources/software/gent/
1. Detection of structural variants in DNA sequences.
2. Graph-based approach for accurate variant identification.
3. Ability to detect various types of variations such as inversions, deletions, insertions, duplications, and translocations.
4. Analysis of structural variations in the human genome.
DNA Comparison, Structural Variants, Genomics https://www.psc.edu/resources/software/gent/ https://www.psc.edu/resources/software/gent/ Bridges-2: https://www.psc.edu/resources/software/gent Bridges-2: 1.0.0 Gent is a graph-based DNA comparison tool that enables the identification of structural variants, inversions, deletions, insertions, duplications, and translocations in the human genome.
geocube Faster Python Library Visualization Tool Physical Sciences Geophysics & Geochemistry Earth & Environmental Sciences 1. Supports visualization of geospatial data in a 3D environment.
2. Allows for interactive exploration of spatial datasets.
3. Enables customization of visual elements such as colors, textures, and annotations.
4. Provides tools for adding interactive controls and user interactions.
5. Compatible with popular geospatial data formats and libraries.
Geospatial Data, 3D Visualization, Python Library Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.0.14-Python-3.8.2 Geocube is a Python library for generating interactive 3D visualizations of geospatial data. It is designed to facilitate the creation of immersive and dynamic representations of geospatial information for research, analysis, and presentation purposes.
geomview Darwin 3D Viewing Visualization Tool Computer & Information Sciences Interactive 3D Viewing Of Objects, Rotation, Translation, Zooming Functionality, Support For Multiple File Formats, Customizable Display Options, Compatibility With Unix Systems 3D Visualization, Interactive Viewing, Unix Software Geomview is an interactive 3D viewing program for Unix. It lets you view and manipulate 3D objects: you use a mouse to rotate, translate, zoom in and out, etc. It reads and writes files in any of the formats supported by your 3D graphics library.
geopandas Aces, Faster Data Analysis Python Library Earth & Environmental Sciences GeoPandas is a project to add support for geographic data to pandas objects. It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and perform geometric operations. Reading & Writing Spatial Data Formats, Spatial Operations & Manipulations, Attribute Joins Between Geospatial Datasets, Handling Of Coordinate Reference Systems (Crs), Visualization Of Geospatial Data Geospatial Data, Python Library, Geospatial Analysis Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.12.2
Faster: 0.8.1-Python-3.8.2
Geopandas is an open-source python library for working with geospatial data, enabling users to easily manipulate and analyze geospatial datasets.
geos Aces, Anvil, Darwin, Expanse, Faster, Ookami Geospatial Software Library Computer & Information Sciences Geographic Information Systems Other Computer & Information Sciences GEOS is a C/C++ library for computational geometry with a focus on algorithms used in geographic information systems (GIS) software. It implements the OGC Simple Features geometry model and provides all the spatial functions in that standard as well as many others.
Description Source: https://libgeos.org/
Geos offers robust support for geometric operations such as buffering, intersection, union, and difference. It provides functionalities for handling various geometric objects like points, lines, polygons, and collections. Geos also includes algorithms for validating geometries and simplifying complex geometric structures. Geometry Engine, Spatial Data Processing, Gis, Open-Source https://libgeos.org/ https://libgeos.org/doxygen/ https://libgeos.org/usage/c_api/
https://libgeos.org/usage/cpp_api/
https://github.com/libgeos/geos/tree/main/examples
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/geos
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 3.9.1, 3.10.3, 3.11.1, 3.12.0
Anvil: 3.8.1, 3.9.1
Expanse: Ad5Oco3
Faster: 3.8.1-Python-3.8.2, 3.9.1, 3.10.3, 3.11.1, 3.12.0
Ookami: Gcc12.1/3.11.0
Geos is an open-source geometry engine that provides C++ software libraries and tools for processing spatial data. It is a key component of the PostGIS spatial database extender and is used in various GIS software applications.
getdist Faster Python Library Data Analysis Physical Sciences Cosmology Astronomy & Planetary Sciences Analysis Of Mcmc Samples, Parameter Estimation In Cosmology, Generation Of Parameter Constraints & Posterior Plots, Computation Of Confidence Limits Mcmc Analysis, Parameter Estimation, Posterior Plots, Cosmology Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.4 GetDist is a Python package for analyzing Monte Carlo Markov Chains (MCMC) samples, primarily used in cosmological parameter estimation. It provides tools for plotting and analyzing MCMC samples, computing confidence limits, and generating parameter constraints and posterior plots.
gethost Ookami Networking Tool Command-Line Utility Computer & Information Sciences 1. Retrieve the IP address and hostname of a domain or URL.
2. Simple and straightforward command-line interface.
3. Useful for network troubleshooting and system administration.
Networking, Command-Line, System Administration Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 1.0 gethost is a command-line utility that retrieves the IP address and hostname of a specified domain or URL. It can be used to quickly obtain network information during troubleshooting or system administration tasks.
getorganelle Anvil Analysis Tool Bioinformatics Tool Biological Sciences Organelle Genomics Genomics Getorganelle is a fast and versatile toolkit for accurate de novo assembly of organelle genomes. De Novo Assembly Of Organelle Genomes, Homology Search, Gene Annotation Bioinformatics, Genomics, Molecular Biology, Computational Biology Anvil: https://www.rcac.purdue.edu/software/getorganelle Anvil: 1.7.7.0 GetOrganelle is a software package that enables de novo assembly, homology search, and gene annotation for organelle genomes.
gettext Aces, Bridges-2, Faster, Kyric Localization Tool Compilers Computer & Information Sciences Gettext is a software framework used for internationalization and localization of software applications, allowing them to be translated into multiple languages. It provides tools for developers to extract strings from their code, create and manage translation files, and compile these files into formats that can be used by the application to display the translated text, thereby making the software accessible to a global audience. Internationalization (I18N), Localization (L10N), Extracting Translatable Strings, Generating Message Catalogs, Translating Strings Internationalization, Localization, Software Development https://www.gnu.org/software/gettext/ https://www.gnu.org/software/gettext/manual/index.html https://www.labri.fr/perso/fleury/posts/programming/a-quick-gettext-tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Bridges-2: https://www.psc.edu/resources/software/gettext
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.21, 0.21.1, 0.22
Bridges-2: 0.22.5-Gcc13.2.1-P20240113
Faster: 0.19.8.1, 0.20.1, 0.21, 0.21.1, 0.22
GNU gettext is a package providing a framework for internationalization and localization of software. It includes tools for extracting translatable strings from source code, for generating message catalogs (pot files), and for translating the strings into different languages.
gfaffix Anvil Computational Tool Bioinformatics Biological Sciences Functional Genomics Genomics GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure. Functional Annotation Of DNA Sequences, Genomic Data Analysis, Identification Of Regulatory Elements, Visualization Tools For Genomic Data Computational Software, Genomic Data Analysis Anvil: https://www.rcac.purdue.edu/software/gfaffix Anvil: 0.1.4 Gfaffix is a computational software package designed for analyzing genomic data, specifically focused on functional annotation and analysis of DNA sequences.
gfastats Anvil Statistical Analysis Tool Python Library Other Mathematics gfastats is a single fast and exhaustive tool for summary statistics and simultaneous *fa* (fasta, fastq, gfa [.gz]) genome assembly file manipulation. Descriptive Statistics, Hypothesis Testing, Regression Analysis, Data Analysis Python Library, Statistical Functions, Data Analysis Anvil: https://www.rcac.purdue.edu/software/gfastats Anvil: 1.2.3, 1.3.6 gfastats is a Python library for statistical functions and data analysis, providing a wide range of functions for descriptive statistics, hypothesis testing, and regression analysis.
gfatools Anvil Tool Bioinformatics Biological Sciences Genetics Biological Sciences gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED. 1. Manipulation of genomic sequence graphs
2. Sequence alignment on graphs
3. Analysis of genome variations within graphs
Genomics, Genome Variation Graphs, Sequence Alignment, Variation Analysis Anvil: https://www.rcac.purdue.edu/software/gfatools Anvil: 0.5 gfatools is a suite of tools for working with genomic sequence graphs and genome variation graphs. It provides functionalities for manipulating genomic graphs, performing sequence alignment on graphs, and analyzing variations within graphs.
gfbf Aces, Faster Compilation Tool Compiler Computer & Information Sciences Artificial Intelligence & Intelligent Systems Computer Science GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. Boolean Function Compilation, Anf To Cnf Conversion, Smt/Sat Translation, Decision Diagram Generation, Truth Table Export Compiler, Boolean Functions, Logic Synthesis, Verification, Optimization Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2022A, 2022B, 2023A, 2023B, 2023.09
Faster: 2022A, 2022B, 2023A
Gfbf is a compiler for Boolean functions, implemented as an SMT/SAT translation tool. It takes a Boolean function expressed as an algebraic normal form (ANF) as input and produces output in various formats including Conjunctive Normal Form (CNF), Decision Diagrams, and Truth Tables. The tool is designed to efficiently manipulate and analyze Boolean functions for various applications in logic synthesis, verification, and optimization.
gffcompare Anvil Computational Tool Bioinformatics Biological Sciences Gffcompare is used to compare, merge, annotate and estimate accuracy of one or more GFF files. Compare, Evaluate, & Classify Transcript Models, Determine Relationships Between Reference Transcripts & Assembled Transcripts, Produce Various Statistics & Visualization Plots For Comparison RNA-Seq, Transcript Assembly, Genome Annotation Anvil: https://www.rcac.purdue.edu/software/gffcompare Anvil: 0.11.2 gffcompare is a tool for evaluating the accuracy of RNA-Seq transcript assemblers and for annotating genomic features.
gffread Anvil Tool Bioinformatics Biological Sciences Gffread is used to validate, filter, convert and perform various other operations on GFF files. 1. Converts GFF3 files to FASTA format. 2. Extracts sequences based on feature type or ID. 3. Translates CDS features to proteins. 4. Supports filtering by attributes or locations. Gff3, Fasta, Sequence Processing Anvil: https://www.rcac.purdue.edu/software/gffread Anvil: 0.12.7 gffread is a tool for converting GFF3 files to FASTA format. It extracts sequences based on feature type or ID, translates CDS features to proteins, and more.
gffutils Anvil Bioinformatics Tool Data Processing & Analysis Biological Sciences Genomics gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. Parsing & Reading Gff Files, Querying Genomic Features, Filtering & Manipulating Gff Data, Converting Gff Files To Different Formats, Integration With Python For Further Analysis Genomic Data, Bioinformatics, Python Library, File Parsing, Data Manipulation Anvil: https://www.rcac.purdue.edu/software/gffutils Anvil: 0.11.1 gffutils is a Python package for working with and manipulating GFF (General Feature Format) files, a tab-delimited file format that stores genomic features. It provides tools for parsing, querying, and analyzing GFF files.
gh Delta, Expanse https://docs.github.com/en/github-cli https://cli.github.com/manual/gh https://docs.github.com/en/github-cli/github-cli/quickstart Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Delta: 2.32.1
Expanse: Eytgnon, Mkz3Uxl
ghostscript Aces, Anvil, Faster Software Development Utility Computer & Information Sciences, Engineering & Technology Ghostscript is an interpreter for the PostScript® language and PDF files. It is available under either the GNU GPL Affero license or licensed for commercial use from Artifex Software, Inc. Ghostscript consists of a PostScript interpreter layer and a graphics library.
Description Source: https://ghostscript.com/
1. Interpret and render PostScript and PDF files
2. Convert files between different formats
3. Manipulate graphics and images
4. Display and print documents
5. Scriptable interface for automation
Document-Processing, File-Conversion, Print-Management https://ghostscript.com/ https://ghostscript.readthedocs.io/en/latest/ https://ghostscript.readthedocs.io/en/latest/Use.html
https://ghostscript.readthedocs.io/en/latest/Source.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/ghostscript
Faster: https://hprc.tamu.edu/software/faster/
Aces: 9.54.0, 9.56.1, 10.0.0, 10.01.2
Anvil: 9.56.1
Faster: 9.52, 9.53.3, 9.54.0, 9.56.1, 10.0.0, 10.01.2
Ghostscript is a versatile software suite for viewing, converting, and printing PostScript and PDF files. It is widely used for rasterizing files for high-quality printing and viewing on a variety of devices.
giflib Aces, Faster Package Giflib is a software package designed for reading and writing GIF (Graphics Interchange Format) images. It provides a set of utilities for processing GIFs, including conversion to and from various formats, making it a valuable tool for developers working with GIF animations and image processing in applications or web services. Reading & Writing Gif Images, Support For Various Gif Image Manipulation Functions, High Performance & Efficient Gif Image Processing, Cross-Platform Compatibility Library, Image Processing, Gif Images https://giflib.sourceforge.net/ https://giflib.sourceforge.net/gif_lib.html https://giflib.sourceforge.net/whatsinagif/index.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.2.1
Faster: 5.2.1
Giflib is a library for reading and writing GIF images. It is a widely used library for handling Graphics Interchange Format (GIF) images in various software applications and programming languages.
gimmemotifs Anvil Bioinformatics Computational Biology Biological Sciences Genetics Biological Sciences GimmeMotifs is a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. 1. De novo motif discovery
2. Motif comparison
3. Scanning for known motifs in DNA sequences
4. Unified framework for running multiple motif discovery tools
5. Merging results to improve motif predictions
Motif Discovery, DNA Sequences, Motif Comparison, Motif Scanning Anvil: https://www.rcac.purdue.edu/software/gimmemotifs Anvil: 0.17.1 Gimmemotifs is a software package for de novo motif discovery, motif comparison and scanning for known motifs in DNA sequences. It provides a unified framework for running multiple motif discovery tools and merging the results to improve motif predictions.
git Aces, Darwin, Delta, Expanse, Faster, Kyric, Ookami Development Tools Version Control System Computer & Information Sciences, Software Engineering, Systems, & Development Git is a distributed version control system, widely used for tracking changes in source code during software development. It allows multiple developers to work collaboratively on a project, providing tools for managing versions, resolving conflicts, and maintaining a history of changes made to the codebase. Distributed Version Control System, Branching & Merging, Security & Encryption, Staging Areas, Collaboration Tools Version Control, Software Development, Source Code Management https://git-scm.com/ https://git-scm.com/docs https://git-scm.com/docs/gittutorial
https://www.youtube.com/watch?v=HVsySz-h9r4
https://www.atlassian.com/git/tutorials
Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.28.0-Nodocs, 2.32.0-Nodocs, 2.33.1-Nodocs, 2.36.0-Nodocs, 2.38.1-Nodocs, 2.41.0-Nodocs, 2.42.0
Delta: 2.39.3
Expanse: Darghpu, Ldetm5Y
Faster: 2.23.0-Nodocs, 2.28.0-Nodocs, 2.32.0-Nodocs, 2.33.1-Nodocs, 2.36.0-Nodocs, 2.38.1-Nodocs, 2.41.0-Nodocs
Ookami: 2.38.1
Git is a distributed version control system designed to handle everything from small to very large projects with speed and efficiency. It is an open-source tool that is widely used for source code management in software development.
git-lfs Aces, Darwin, Delta, Expanse, Faster Development Tool Version Control System Engineering & Technology Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise. Efficient Handling Of Large Files, Reduced Impact Of Large Files In Repositories, Text Pointers For Large Files While Storing In Remote Server, Seamless Integration With Git Version Control, File Storage, Git Extension https://git-lfs.com/ https://github.com/git-lfs/git-lfs/tree/main/docs https://github.com/git-lfs/git-lfs/wiki/Tutorial
https://github.com/git-lfs/git-lfs/wiki
Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.2.0, 3.3.0
Delta: 3.3.0
Expanse: Kmruniy, 32Gm6Hi
Faster: 3.2.0, 3.4.0
Git Large File Storage (LFS) is a Git extension that reduces the impact of large files in your repository by replacing them with text pointers while storing the actual file content on a remote server. It seamlessly integrates with Git and provides efficient handling of large files, making it easier to work with version-controlled repositories containing large assets.
gitpython Faster Development Library Computer Science 1. Ability to interface with Git repositories within Python scripts
2. Supports common Git operations like cloning, committing, pushing, and pulling
3. Provides access to Git's objects (commits, trees, blobs) and references (branches, tags)
4. Offers options for working with submodules and managing repository information
Version Control, Source Code Management, Python Library Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.1.27 GitPython is a python library used to interact with Git repositories. It provides a high-level API that allows for interfacing with Git commands and repositories directly from Python scripts.
gklib Aces, Stampede3 Computational Software Library Mathematics Computational Geometry Applied Mathematics A library of various helper routines and frameworks used by Karypis Lab software such as METIS. The core features of gklib include robust and reliable geometric algorithms for tasks such as intersection detection, proximity queries, convex hull computation, point location, and triangulation. Geometric Kernels, Computational Geometry, Algorithms Aces: https://hprc.tamu.edu/software/aces/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 5.1.1, 20231211, 20240119, 20240321, 20240329
Stampede-3: Git20240111
gklib is a C++ library for geometric kernels that provides efficient and accurate geometric algorithms for computational geometry and related fields.
gl2ps Aces, Faster Library GL2PS is a C library providing high quality vector output for any OpenGL application. The main difference between GL2PS and other similar libraries is the use of sorting algorithms capable of handling intersecting and stretched polygons, as well as non manifold objects. GL2PS provides advanced smooth shading and text rendering, culling of invisible primitives, mixed vector/bitmap output, and much more...
Description Source: https://www.geuz.org/gl2ps/
1. Conversion of OpenGL graphics to PostScript format
2. Support for 2D and 3D graphics
3. Integration with existing OpenGL applications
4. Vector-based output for high-quality printing
5. Cross-platform compatibility
Opengl, Postscript, Printing, Graphics, Vector Graphics https://www.geuz.org/gl2ps/ https://www.geuz.org/gl2ps/#tth_sEc2 https://www.geuz.org/gl2ps/#tth_sEc3
https://www.geuz.org/gl2ps/#tth_sEc4
https://github.com/Open-Cascade-SAS/gl2ps/blob/occt-emf/gl2psTest.c
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.4.2
Faster: 1.4.2
GL2PS is an OpenGL to PostScript printing library that converts any OpenGL action into a vector PostScript image. It provides capabilities for saving OpenGL-generated 2D and 3D graphics as encapsulated PostScript files. GL2PS is written in C++ and can be easily integrated into existing OpenGL code.
glew Aces, Faster Tool Library Computer Science The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. 1. Cross-platform support
2. Dynamic loading of OpenGL extensions
3. Lightweight and easy to use
4. Simplifies managing OpenGL extensions
5. Open-source with a permissive license
Opengl, Extension Loader, C/C++ Library Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.2.0-Egl
Faster: 2.2.0-Egl, 2.2.0-Osmesa
The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. It assists in accessing OpenGL extensions and functions dynamically, providing a simple and lightweight solution for managing OpenGL extensions.
glfw Aces, Faster Development Tool Library Computer & Information Sciences GLFW is an Open Source, multi-platform library for OpenGL, OpenGL ES and Vulkan development on the desktop. It provides a simple API for creating windows, contexts and surfaces, receiving input and events.
Description Source: https://www.glfw.org/
Cross-Platform Window Creation & Management, Opengl Context Creation, Input Handling (Keyboard, Mouse, Gamepad), Event Callbacks, Monitor Handling For Fullscreen Windows, File & Drag-&-Drop Support Graphics, Opengl, Cross-Platform, Window Management, Input Handling https://www.glfw.org/ https://www.glfw.org/docs/latest/ https://www.glfw.org/docs/latest/quick.html
https://www.glfw.org/docs/latest/intro_guide.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.8
Faster: 3.3.4, 3.3.8
GLFW is an open-source, multi-platform library for creating windows with OpenGL contexts and managing input. It provides a simple API for creating and managing windows, contexts, and surfaces, receiving input events. GLFW is written in C and provides native support for Windows, macOS, and Linux, as well as experimental support for mobile platforms.
glib Aces, Faster Utility Library Computer & Information Sciences GLib is a general-purpose, portable utility library, which provides many useful data types, macros, type conversions, string utilities, file utilities, a mainloop abstraction, and so on. It is one of the base libraries of GTK+.
Description Source: https://docs.gtk.org/glib/
Data Structure Handling For Lists, Trees, & Hashes, Memory Management & Allocation, Thread Support, Internationalization Support, Dynamic Loading Of Modules, Utilities For Strings & File Manipulation Utility Library, C Programming, Data Structures, Memory Management, Thread Support https://gitlab.gnome.org/GNOME/glib/ https://docs.gtk.org/glib/ https://docs.gtk.org/glib/programming.html
https://docs.gtk.org/glib/types.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.66.1, 2.68.2, 2.69.1, 2.72.1, 2.75.0, 2.77.1
Faster: 2.62.0, 2.64.1, 2.66.1, 2.68.2, 2.69.1, 2.72.1, 2.75.0, 2.77.1
GLib is a general-purpose utility library for the C programming language. It provides data structure handling for lists, trees, hashes, memory allocation, and other commonly needed functionality.
glib-networking Aces, Faster Computer & Information Sciences Network extensions for GLib High-Level Network Access, Network Diagnostic Utilities, Tls Support Glib, Network, Linux, Library Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.72.1
Faster: 2.72.1
Glib-networking is a set of network-related GIO modules for GLib, providing high-level network access, network diagnostic utilities, and TLS support. It is part of the GNOME project and is commonly used in Linux-based systems.
glibc Ookami Library System Library Computer & Information Sciences Systems Programming Computer & Information Sciences Implementation Of The Standard C Library Functions, System Calls & Low-Level Interfaces, Dynamic Memory Allocation & Management, Thread Support & Synchronization, Localization Support C Library, Operating System, System Programming Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 2.34 glibc, the GNU C Library, is an essential part of most systems running the Linux kernel. It provides the necessary functionality for programs written in the C programming language to interact with the operating system and hardware.
glimmer Anvil Gene Prediction Tool Bioinformatics Biological Sciences Microbial Genomics Genomics Glimmer is system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. 1. Gene prediction based on statistical models and hidden Markov models.
2. Specifically tailored for microbial genomes.
3. Supports both bacterial and archaeal genomes.
4. Provides predictions for protein-coding genes.
Gene Prediction, Microbial Genomes, Hidden Markov Models Anvil: https://www.rcac.purdue.edu/software/glimmer Anvil: 3.02 Glimmer is a gene prediction software tool designed for microbial genomes. It uses a combination of statistics and hidden Markov models to predict potential protein-coding genes in DNA sequences.
glimmerhmm Anvil Bioinformatics Tool Gene Prediction Biological Sciences Microbial Genomics Genomics Glimmerhmm is a new gene finder based on a Generalized Hidden Markov Model. Gene Prediction In Microbial Genomes, Utilizes Hidden Markov Models, Predicts Start & Stop Codons, & Exons, Accurate Gene Location Prediction Gene Prediction, Microbial Genomes, Hidden Markov Models, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/glimmerhmm Anvil: 3.0.4 GlimmerHMM is a software system for gene prediction in microbial genomes. It uses hidden Markov models to represent various aspects of a gene (e.g., start codons, stop codons, and exons) to accurately predict the locations of genes.
glm Aces, Delta Library Statistical Analysis Mathematics Statistics & Probability The GLM (OpenGL Mathematics) library is a header-only C++ library designed for graphics software development, providing a wide range of mathematical structures and functions. Inspired by the syntax and conventions of GLSL (OpenGL Shading Language), GLM is particularly useful for OpenGL applications, offering functionality for vectors, matrices, and other complex mathematical operations needed in 3D graphics programming. Implementation Of Generalized Linear Models (Glm), Support For Various Exponential Family Distributions, Estimation Of Model Parameters, Prediction & Inference, Model Evaluation & Diagnostics Python Library https://glm.g-truc.net/0.9.9/ https://glm.g-truc.net/0.9.9/api/modules.html https://github.com/g-truc/glm/blob/0.9.9.2/doc/manual.pdf
https://www.youtube.com/watch?v=F0vUESYIrno
https://web.engr.oregonstate.edu/~mjb/cs491/Handouts/GLM.1pp.pdf
Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Aces: 0.9.9.8
Delta: 0.9.9.8
glm is a Python library for Generalized Linear Models (GLM) with support for exponential family distributions.
glnexus Anvil Bioinformatics Tool Genomic Data Analysis Biological Sciences Glnexus: Scalable gVCF merging and joint variant calling for population sequencing projects. - Haplotype-aware variant calling
- Genotyping in large cohorts
- Detects complex variants
- Scalable to handle large datasets
- Supports VCF and BCF formats
Variant Calling, Genotyping, Haplotype-Aware, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/glnexus Anvil: 1.4.1 glnexus is a software tool for haplotype-aware variant calling and genotyping in large cohorts.
globalarrays Aces, Faster Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.8.2
Faster: 5.8, 5.8.2
globus-cli Aces, Faster Command Line Tool Tools Other Computer & Information Sciences A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. Manage File Transfers, Access Endpoints, Monitor Tasks, Interact With Globus Service Command-Line Interface, File Transfer Service, Data Management, Data Transfer Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.6.0
Faster: 3.6.0
The globus-cli is a command-line interface tool that provides users with a way to interact with the Globus file transfer service directly from the terminal. It allows for managing transfers, accessing endpoints, and monitoring tasks efficiently through the command line interface.
glpk Aces, Darwin, Expanse, Faster Mathematical Optimization Solver Mathematics Operations Research Applied Mathematics The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
Description Source: https://www.gnu.org/software/glpk/
Solves Large-Scale Linear Programming Problems, Supports Mixed Integer Programming & Related Problems, Offers Both A High-Level & Low-Level C Api For Problem Input & Output, Includes Tools For Post-Processing & Sensitivity Analysis Linear Programming, Optimization, Open-Source https://www.gnu.org/software/glpk/ http://most.ccib.rutgers.edu/glpk.pdf https://martin-thoma.com/how-to-use-glpk/
https://en.wikibooks.org/wiki/GLPK/Using_the_GLPK_callable_library
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.0
Expanse: 2266Fla
Faster: 4.65, 5.0
GNU Linear Programming Kit (GLPK) is an open-source software package for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is designed with an emphasis on flexibility, portability, and ease of use.
gmap Anvil Bioinformatics Tool Alignment Tool Biological Sciences Transcriptomics Genomics Gmap is a genomic mapping and alignment program for mRNA and EST sequences. Efficient Mapping & Alignment Of Cdna Sequences To Genomes, Identification Of Exon Junctions, Suitable For Analyzing RNA-Seq Data, Highly Accurate Mapping Results Bioinformatics, Computational Biology, Genomics, Transcriptomics, RNA-Seq Anvil: https://www.rcac.purdue.edu/software/gmap Anvil: 2021.05.27, 2021.08.25 GMAP (Genomic Mapping and Alignment Program) is a highly efficient and accurate software for mapping and aligning cDNA sequences to a genome, particularly useful in the analysis of RNA-seq data. It is designed to identify and map exon junctions in large genomes.
gmap-gsnap Expanse Analysis Tool Bioinformatics Biological Sciences Genetics Biological Sciences Splice-Aware RNA-Seq Read Mapping, Alignment To A Reference Genome, Identification Of Novel Splice Sites, Support For Gapped Alignment RNA-Seq, Bioinformatics, Mapping, Alignment Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 2020-06-01 GMAP and GSnap are splice-aware algorithms for mapping RNA-Seq reads to a genome. GMAP is a genomic mapping and alignment program while GSnap is a sensitive and accurate gapped read mapper. Both tools are commonly used in bioinformatics for RNA-Seq analysis.
gmp Aces, Anvil, Darwin, Expanse, Faster, Kyric, Ookami Library Library Mathematics Other Mathematics Pure Mathematics GNU MP is a portable library written in C for arbitrary precision arithmetic on integers, rational numbers, and floating-point numbers. It aims to provide the fastest possible arithmetic for all applications that need higher precision than is directly supported by the basic C types.
Description Source: https://gmplib.org/manual/Introduction-to-GMP
1. High-performance arithmetic functions for integers, rationals, and floating-point numbers.
2. Support for a wide range of mathematical operations including addition, subtraction, multiplication, division, exponentiation, and more.
3. Efficient memory management and algorithms for large numbers.
4. Portable and easy to use C library with interfaces available for various programming languages.
Computational Software, Library, Mathematics, Software Development https://gmplib.org/ https://gmplib.org/manual/ https://gmplib.org/manual/GMP-Basics
https://gmplib.org/pi-with-gmp
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gmp
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 6.2.0, 6.2.1, 6.3.0
Anvil: 6.2.1
Expanse: 6.1.2
Faster: 6.1.2, 6.2.0, 6.2.1
The GNU Multiple Precision Arithmetic Library (GMP) is a free library for arbitrary-precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers.
gmpy2 Aces, Faster Python Library Library Computer & Information Sciences GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x 1. High-performance multiple-precision arithmetic
2. Arbitrary-precision integer arithmetic
3. Arbitrary-precision floating-point arithmetic
4. Compatible with Python's math module
5. Supports complex numbers and mathematical functions
Python Library, Arbitrary-Precision Arithmetic, Gmp Library, Mpfr Library Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.1.2, 2.1.5
Faster: 2.1.0B4, 2.1.2, 2.1.5
gmpy2 is a Python library for arbitrary-precision arithmetic within Python using the GMP and MPFR libraries. It provides efficient multiple-precision arithmetic in Python and supports both integer and floating-point arithmetic with arbitrary precision.
gmt Anvil Command Line Tool Visualization & Modeling Earth & Environmental Sciences GMT is a collection of freely available command-line tools under the GNU LGPL that allows you to manipulate x, y and x, y, z data sets (filtering, trend fitting, gridding, projecting, etc.) and produce illustrations ranging from simple x-y plots, via contour maps, to artificially illuminated surfaces and 3-D perspective views in black/white or full color.
Description Source: https://docs.generic-mapping-tools.org/latest/gmt.html
Manipulating Geographic & Cartesian Data Sets, Producing Postscript Illustrations, Supports Over 40 Map Projections & Transformations, Includes Coastlines, Rivers, & Political Boundaries Data Mapping, Geographic Data, Cartesian Data, Illustration, Postscript, Map Projections https://www.generic-mapping-tools.org/ https://docs.generic-mapping-tools.org/latest/ https://docs.generic-mapping-tools.org/latest/tutorial.html
https://www.generic-mapping-tools.org/workshops/#past-workshops
Anvil: https://www.rcac.purdue.edu/software/gmt Anvil: 6.1.0 The Generic Mapping Tools (GMT) is an open-source collection of command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots through contour maps to artificially illuminated surfaces and 3-D perspective views. GMT supports over 40 map projections and transformations and comes with support data such as coastlines, rivers, and political boundaries.
gnu-parallel Ookami GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input. The typical input is a list of files, a list of hosts, a list of users, a list of URLs, or a list of tables. A job can also be a command that reads from a pipe. GNU parallel can then split the input and pipe it into commands in parallel.
Description Source: https://www.gnu.org/software/parallel/
https://www.gnu.org/software/parallel/ https://www.gnu.org/software/parallel/sphinx.html https://www.gnu.org/software/parallel/parallel_tutorial.html
https://www.gnu.org/software/parallel/parallel_examples.html
https://www.gnu.org/software/parallel/parallel_cheat.pdf
https://zenodo.org/records/1146015
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 20220922
gnu9 Kyric Compiler https://gcc.gnu.org/ https://gcc.gnu.org/onlinedocs/gcc-13.2.0/gcc/ https://gcc.gnu.org/wiki/GettingStarted
https://gcc-newbies-guide.readthedocs.io/en/latest/
https://www.geeksforgeeks.org/gcc-command-in-linux-with-examples/
Kyric: 9.3.0
gnuplot Aces, Anvil, Darwin, Delta, Expanse, Faster, Ookami Plotting & Data Visualization Graphing & Visualization Tools Physical Sciences Engineering gnuplot is a command-driven plotting program. It can be used interactively to plot functions and data points in both two- and three-dimensional plots in many different styles and many different output formats. Gnuplot can also be used as a scripting language to automate generation of plots.
Description Source: http://www.gnuplot.info/faq/#x1-60001.1
Gnuplot enables users to generate 2D and 3D plots, histograms, and animations. It supports a wide range of functions and data sources, with the ability to customize plot styles, labels, and axes. Gnuplot can be scripted for batch processing and supports various file formats for output including PNG, PDF, and SVG. It also allows users to combine multiple plots and perform complex data manipulations. Graphing, Visualization, Data Analysis https://gnuplot.sourceforge.net/ http://gnuplot.info/docs_5.5/Overview.html https://gnuplot.sourceforge.net/screenshots/index.html#demos
https://gnuplot.sourceforge.net/help.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gnuplot
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 5.4.4, 5.4.6, 5.4.8
Anvil: 5.4.2
Delta: 5.4.3
Expanse: Lfaey6L, Mfinpvw
Faster: 5.2.8, 5.4.1, 5.4.2, 5.4.4
Ookami: 5.4.5
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms. It is capable of producing interactive plots and supports various output formats.
gnutls Aces, Faster Library Networking & Security Computer & Information Sciences GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. Implement Ssl, Tls, & Dtls Protocols, Support Various Cryptographic Algorithms, Secure Communication Library Security, Encryption, Networking Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.7.3
Faster: 3.7.3
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols, providing various cryptographic algorithms.
go Aces, Darwin, Expanse, Faster, Kyric, Ookami Programming Language Go is expressive, concise, clean, and efficient. Its concurrency mechanisms make it easy to write programs that get the most out of multicore and networked machines, while its novel type system enables flexible and modular program construction. Go compiles quickly to machine code yet has the convenience of garbage collection and the power of run-time reflection. It's a fast, statically typed, compiled language that feels like a dynamically typed, interpreted language.
Description Source: https://go.dev/doc/
https://go.dev/ https://go.dev/doc/ https://go.dev/doc/tutorial/getting-started
https://go.dev/doc/tutorial/create-module
https://go.dev/doc/tutorial/workspaces
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 1.18.3
Expanse: 1.15.1
Faster: 1.17.6, 1.18.3, 1.19.1, 1.20.5, 1.21.2
Ookami: 1.21.4
go-bootstrap Kyric Template Project Development Tools Engineering & Technology Software Engineering, Systems, & Development 1. Predefined project structure for Go applications. 2. Built-in configuration setup. 3. Integration with popular Go libraries. 4. Simplifies starting a new Go project. Go, Template, Project Structure, Best Practices https://go.dev/ https://go.dev/doc/ https://go.dev/doc/tutorial/getting-started
https://go.dev/doc/tutorial/create-module
https://go.dev/doc/tutorial/workspaces
go-bootstrap is a Go programming language template project that provides a starting point for building Go applications with a predefined project structure, configuration, and best practices.
goatools Anvil Python Library Library Biological Sciences Genetics Bioinformatics Goatools is a Python library for Gene Ontology analyses. Interpretation Of Gene Ontology (Go), Statistical Analysis Of Go Term Enrichment, Visualization Of Go Term Relationships, Integration With Biological Data Analysis Pipelines Bioinformatics, Python Library, Gene Ontology, Enrichment Analysis, Biological Data Analysis Anvil: https://www.rcac.purdue.edu/software/goatools Anvil: 1.1.12, 1.2.3 Goatools is a Python library for exploring the Gene Ontology and determining the statistical significance of GO term enrichment in sets of genes or gene products.
gobff Faster Computational Software Molecular Modeling Biological Sciences Protein Structure Prediction Bioinformatics 1. Fragment-Assembly Monte Carlo (FAMC) based protein structure prediction
2. Fragment assembly for structure modeling
3. Monte Carlo simulations for model refinement
4. Ability to predict protein structures with high accuracy
5. User-friendly interface for easy input and visualization of results
Protein Structure Prediction, Fragment Assembly, Monte Carlo Simulations Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020B, 2021A gobff is a software tool for protein structure prediction based on the Fragment-Assembly Monte Carlo (FAMC) approach. It enables the modeling of protein structures by assembling fragments and refining the models using Monte Carlo simulations.
gobject-introspection Aces, Faster Library Middleware Computer & Information Sciences Computer Science GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate metadata files, in addition to the actual native C library. Then language bindings can read this metadata and automatically provide bindings to call into the C library.
Description Source: https://gi.readthedocs.io/en/latest/
Automated Generation Of Language Bindings For C Libraries, Allows Scripting Languages & Other Environments To Access C Libraries Easily, Eliminates Manual Intervention In Creating Language Bindings, Supports Gobject-Based Libraries Middleware, Language Bindings, Automation, Compatibility https://gitlab.gnome.org/GNOME/gobject-introspection/ https://gi.readthedocs.io/en/latest/ https://gitlab.gnome.org/GNOME/gobject-introspection/-/tree/main/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.68.0, 1.72.0, 1.74.0, 1.76.1
Faster: 1.63.1-Python-3.7.4, 1.64.0-Python-3.8.2, 1.66.1, ...
GObject Introspection is a middleware layer between C libraries (using GObject) and language bindings. The goal is to make the C libraries accessible from scripting languages and other environments without the need for manual intervention.
golang Darwin Systems Programming Programming Language Computer & Information Sciences Memory Safety, Garbage Collection, Static Typing, Concurrency Support Programming Language, Software Development, Systems Programming Go, also commonly referred to as Golang, is a statically typed, compiled programming language designed at Google. It has a syntax similar to C, but with memory safety, garbage collection, structural typing, and CSP-style concurrency.
gompi Aces, Faster Engineering & Technology Gompi is a software toolchain that combines the GNU Compiler Collection (GCC) for compiling software, OpenMPI for supporting parallel computing that requires message passing, and other essential libraries and tools for scientific computing. It is designed to facilitate the development and execution of high-performance computing (HPC) applications, especially those requiring robust parallel processing capabilities across clusters and grids. Supports Mpi For Developing Parallel Applications, Includes Compilers & Libraries For Efficient Execution On Hpc Clusters, Optimizes Communication & Coordination Between Computing Nodes, Facilitates High-Performance Computing For Scientific & Engineering Simulations Hpc, Parallel Computing, Mpi, Distributed Computing https://docs.easybuild.io/api/easybuild/toolchains/gompi/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2020B, 2021A, 2021B, 2022A, 2022B, 2023A, 2023B, 2023.05, 2023.09
Faster: 2018B, 2019B, 2020A, 2020B, 2021A, 2021B, 2022A, 2022B, 2022.05, 2023A, 2023B
Gompi is a parallel computing software tool that provides a set of compilers and libraries for running MPI (Message Passing Interface) programs on HPC (High Performance Computing) clusters. It aims to enhance the performance of parallel applications by optimizing communication and coordination between nodes in distributed computing environments.
gompic Aces, Faster Research Simulation Framework Physical Sciences Granular Materials Simulation Other Physical Sciences GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
Description Source: https://hprc.tamu.edu/software/aces/
1. Simulation of granular systems with complex interactions.
2. Study of collective dynamics and emergent behaviors in soft matter.
3. Analysis of granular flow, pattern formation, and self-organization.
4. Open-source and customizable framework for research purposes.
Simulation, Granular Materials, Collective Dynamics, Soft Matter https://docs.easybuild.io/api/easybuild/toolchains/gompic/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2020B
Faster: 2019B, 2020A, 2020B
gompic is an open-source framework for simulating collective dynamics in soft matter systems with a focus on granular materials. It is designed to simulate the dynamics of large ensembles of particles undergoing complex interactions and can be used to study phenomena like granular flow, pattern formation, and self-organization.
googletest Aces, Faster Library Testing Framework Computer & Information Sciences GoogleTest is Google’s C++ testing and mocking framework.
Description Source: https://google.github.io/googletest/
Supports Various Testing Styles (Functional, Fixture, Parameterized, Etc.), Rich Set Of Assertion Macros For Validating Test Outcomes, Automatic Test Discovery & Registration, Integration With The Google C++ Testing Framework For Advanced Features, Reusable Test Fixtures For Common Setup & Teardown Operations Unit Testing, C++ Testing, Testing Library, Software Testing https://github.com/google/googletest https://google.github.io/googletest/ https://google.github.io/googletest/primer.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.11.0, 1.12.1, 1.13.0
Faster: 1.10.0, 1.11.0, 1.12.1, 1.13.0
Google Test is a unit testing library for the C++ programming language. It is designed to be easy to write and understand tests, provides a rich set of assertions for verifying test expectations, and supports various testing styles.
gpaw Anvil Simulation Computational Chemistry Physical Sciences Materials Science Condensed Matter Physics GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). 1. Efficient and accurate electronic structure calculations using DFT.
2. Implementation of the projector-augmented wave (PAW) method.
3. Parallelized computations for high-performance calculations.
4. Support for a wide range of systems including atoms, molecules, and solid materials.
5. Ability to handle large systems with scalability.
6. Integration with various post-processing and analysis tools for comprehensive data analysis.
Dft, Electronic Structure, Quantum Mechanics https://gitlab.com/gpaw/gpaw https://wiki.fysik.dtu.dk/gpaw/documentation/documentation.html https://wiki.fysik.dtu.dk/gpaw/tutorialsexercises/tutorialsexercises.html
https://wiki.fysik.dtu.dk/gpaw/documentation/basic.html
Anvil: https://www.rcac.purdue.edu/software/gpaw Anvil: 21.1.0 GPAW (Grid-based Projector-augmented wave method) is an efficient and accurate Density Functional Theory (DFT) code based on the projector-augmented wave (PAW) method. It is designed for simulating the electronic structure of atoms, molecules, and solid materials.
gperf Aces, Faster, Ookami Compiler/Generator Development Tool Computer & Information Sciences Software Engineering, Systems, & Development Computer Science GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
Description Source: https://www.gnu.org/software/gperf/
1. Generates perfect hash functions
2. Optimized for constructing minimal perfect hash tables
3. Supports sets of keys for hash function generation
Perfect Hash Function, Hash Table, Optimization, Gnu https://www.gnu.org/software/gperf/ https://www.gnu.org/software/gperf/manual/gperf.html https://developer.ibm.com/tutorials/l-gperf/
https://www.math.utah.edu/docs/info/gperf_5.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 3.1
Faster: 3.1
Ookami: 3.1
GNU gperf is a perfect hash function generator tool that generates perfect hash functions for sets of keys, optimized for use in constructing a minimal perfect hash table.
gperftools Aces, Faster, Ookami Tool Performance Analysis & Profiling Tools Engineering & Technology Gperftools, formerly known as Google Performance Tools, is a collection of utilities for measuring and improving the performance of C++ programs. The suite includes a high-performance, multi-threaded malloc implementation, as well as tools for heap profiling, heap checking, and CPU profiling, making it valuable for developers looking to optimize their applications for speed and memory usage. 1. CPU profiler for single-threaded and multithreaded applications.
2. Heap profiler for memory allocation analysis.
3. Heap-checker for detecting memory leaks and memory errors.
4. Performance analysis tools to aid in optimizing code performance.
5. Scalable and efficient profiling capabilities for large-scale applications.
Performance Analysis, Profiling, C/C++ https://github.com/gperftools/gperftools https://github.com/gperftools/gperftools/wiki#documentation https://github.com/gperftools/gperftools/wiki#example
https://developer.ridgerun.com/wiki/index.php/Profiling_with_GPerfTools
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.10, 2.13
Faster: 2.12, 2.13, 2.14
Ookami: 2.9.1
gperftools is a collection of performance analysis and profiling tools for C and C++ applications. It includes tools such as CPU and heap profilers, heap-checker, and a specialized CPU profiler for multithreaded programs.
gpflow Aces, Faster Computational Software Computer & Information Sciences, Artificial Intelligence & Intelligent Systems GPflow is a package for building Gaussian process models in python, using TensorFlow. 1. Supports Gaussian Processes (GPs) and Bayesian Neural Networks (BNNs)
2. High-level abstractions for creating complex models
3. Scalable inference methods for efficient computation
4. Integration with TensorFlow for automatic differentiation
5. Modular design for easy customization and extension
Machine Learning, Probabilistic Programming, Gaussian Processes Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.9.0-Cuda-11.7.0-Tensorflow-2.11.0, 2.9.0-Cuda-11.7.0
Faster: 2.9.0-Cuda-11.7.0-Tensorflow-2.11.0
GPflow is a Gaussian process library that uses TensorFlow for its core computational backend. It is a scalable, flexible, and modular Gaussian process framework for building probabilistic models.
gpu Expanse Hardware Intermediate Engineering & Technology, Computer & Information Sciences Infrastructure & Instrumentation 1. Parallel processing: GPU architecture allows for thousands of cores to run multiple tasks simultaneously.
2. High-speed memory: They have dedicated high-speed memory to handle massive datasets efficiently.
3. Accelerated computing: GPUs speed up various computational tasks, including machine learning, simulations, and scientific calculations.
4. Programming support: GPU programming frameworks like CUDA and OpenCL enable developers to leverage GPU processing power in their applications.
Software, Computational Software, Hpc Tools, Gpu, Parallel Processing Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 0.15.4, 0.17.3B GPU, short for Graphics Processing Unit, is a specialized electronic circuit designed to rapidly manipulate and alter memory to accelerate the creation of images in a frame buffer intended for output to a display device. In recent years, GPUs have been leveraged for general-purpose computing, allowing for massive parallel processing capabilities.
gpustat Aces, Faster Library Data Management & Analytics Engineering & Technology Computer & Information Sciences Computer Science Gpustat is a command-line utility that provides a quick and concise overview of the GPU status and usage information on systems with NVIDIA GPUs. It displays critical details such as GPU utilization, memory usage, temperature, and the list of processes currently using the GPUs, making it an essential tool for monitoring and managing GPU resources in real-time for both development and production environments. Retrieve Gpu Status Information, Monitor Gpu Utilization, Check Memory Usage & Temperature Of Gpus, Access Power Consumption Data, Simple Command-Line Interface For Quick Status Checks Gpu Monitoring, System Administration, Python Library, Command-Line Tool https://github.com/wookayin/gpustat https://github.com/wookayin/gpustat#usage https://github.com/wookayin/gpustat#tips Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.1
Faster: 0.6.0, 1.0.0B1, 1.1
gpustat is a Python library that gives an easy access to the GPU-related data, such as GPU utilization, memory usage, temperature, and power. It provides a command-line interface for quickly checking the status of GPUs in a system.
gpy Faster Data Analysis Library Computer & Information Sciences Gaussian Process Regression, Gaussian Process Classification, Gaussian Process Optimization, Implementation In Python Machine Learning, Data Analysis, Python, Gaussian Processes Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.10.0 GPy is a Gaussian process framework in Python for implementing Gaussian processes. It offers tools for Gaussian process regression, classification, optimization, and more.
gpytorch Faster Python Library Machine Learning Library Computer & Information Sciences 1. Scalable Gaussian process models
2. Integration with PyTorch for deep learning
3. Flexibility in model construction
4. Efficient computation through GPU acceleration
5. Bayesian optimization and kernel learning capabilities
Machine Learning, Gaussian Processes, Deep Learning Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.6.0 GPyTorch is a Gaussian process library implemented using PyTorch. It is designed for scalable and flexible Gaussian process models, with a focus on deep learning integration.
graalvm Faster Compiler/Runtime Development Tools Computer & Information Sciences Support For Multiple Languages Like Java, Javascript, Python, Ruby, R, & Llvm-Based Languages, High-Performance Runtime With Enhanced Application Performance, Just-In-Time Compilation For Improved Efficiency, Polyglot Capabilities Allowing Interoperability Between Different Languages, Native Image Generation For Faster Startup & Lower Memory Consumption Software Development, Runtime Environment, Polyglot Programming, Just-In-Time Compilation, Native Image Generation Faster: https://hprc.tamu.edu/software/faster/ Faster: 21.3.0, 22.2.0 GraalVM is a high-performance runtime providing significant improvements in application performance and efficiency. It is designed to run applications written in Java, JavaScript, LLVM-based languages, Python, Ruby, R, and other dynamic languages.
grace Expanse Graphing/Plotting Data Visualization/Plotting Physical Sciences Some core features of Grace include the ability to create both 2D and 3D plots, support for various plot types (e.g., line, scatter, bar), customizable plot properties (e.g., colors, labels, legends), interactive plot manipulation, export options for different file formats, and scripting capabilities for automation. Plotting Tool, Scientific Visualization, 2D Plotting, Engineering Applications Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: 5.1.25 Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. The program renders high-quality plots for scientific and engineering applications.
gradle Faster Tools Build Tools Computer & Information Sciences Support For Multi-Project Builds, Dependency Management, Plugins For Various Tasks, Incremental Builds, Extensible Through Groovy Dsl Build Automation, Dependency Management, Java, Groovy Faster: https://hprc.tamu.edu/software/faster/ Faster: 6.9.1 Gradle is an open-source build automation tool focused on flexibility and performance. It uses a Groovy-based domain-specific language (DSL) to define build configurations, allowing for highly customizable build processes.
grads Anvil Desktop Application Visualization Software Earth & Environmental Sciences Data Visualization, Data Analysis, Grid Analysis, Time Series Analysis, Meteorological Data Processing, Customizable Plots Data Visualization, Meteorology, Climatology, Earth Science, Data Analysis Anvil: https://www.rcac.purdue.edu/software/grads Anvil: 2.2.1 GrADS (Grid Analysis and Display System) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. It is particularly popular in meteorology and climatology for analyzing and plotting meteorological data.
graphblas Aces Library Computational Software Computer & Information Sciences SuiteSparse:GraphBLAS is a complete implementation of the GraphBLAS standard, which defines a set of sparse matrix operations on an extended algebra of semirings using an almost unlimited variety of operators and types. When applied to sparse adjacency matrices, these algebraic operations are equivalent to computations on graphs. 1. Extensive set of linear algebra operations for manipulating graph structures and sparse matrices.
2. Optimized for performing calculations on large-scale graphs efficiently.
3. Provides a flexible framework for developing graph algorithms and applications.
4. Supports a wide range of graph analytics and machine learning tasks.
5. Designed for parallel and distributed computing environments.
Graph, Linear Algebra, Sparse Matrices Aces: https://hprc.tamu.edu/software/aces/ Aces: 8.2.1 GraphBLAS is a collection of high-performance linear algebraic operations specifically designed for sparse graphs and matrices.
graphene Aces, Faster Library Web Development Computer & Information Sciences Graphene is a software library that provides a collection of utilities for handling 2D graphics and computational geometry, focusing on providing a thin layer of types and functions that are useful for graphics applications. It is designed to be efficient and lightweight, offering capabilities such as matrices, vectors, rectangles, and quaternions for operations like transformations and intersections, making it a valuable tool for developers working on graphical interfaces, animations, and other visual computations. 1. Simplifies the process of building GraphQL APIs
2. Integrates seamlessly with Python-based web frameworks
3. Provides a simple and elegant syntax for defining GraphQL schemas
4. Supports auto-generated documentation
Python Library, Graphql https://ebassi.github.io/graphene/ https://ebassi.github.io/graphene/docs/ https://github.com/ebassi/graphene/wiki/Using-Graphene-from-Python Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.10.8
Faster: 1.10.8
Graphene is a Python library for building GraphQL APIs fast and easily.
graphicsmagick Aces, Faster Image Processing Software Other Computer & Information Sciences GraphicsMagick is a robust and efficient software suite for processing images, offering a rich set of command-line utilities and programming APIs for reading, writing, and manipulating an array of image formats. Renowned for its performance and quality, it supports tasks such as resizing, rotating, and color adjustments, making it a versatile tool for developers, photographers, and graphic artists in automating image processing workflows. Support For Over 88 Major Image Formats, Image Processing Capabilities, Extensive Command-Line Tools, Efficient Handling Of Large Images, Color Management & Color Space Conversion Image Processing, Graphics, Media Editing, Command-Line Tools http://www.graphicsmagick.org/ http://www.graphicsmagick.org/GraphicsMagick.html http://www.graphicsmagick.org/programming.html
https://www.tutorialspoint.com/graphicsmagick-a-powerful-image-processing-cli-tool-for-linux
https://www.tecmint.com/graphicsmagick-image-processing-cli-tool-for-linux/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.3.36
Faster: 1.3.36
GraphicsMagick is a robust collection of tools and libraries that offers a comprehensive range of image processing capabilities. It provides a powerful utility for dynamically reading, writing, and modifying images for over 88 major formats.
graphite2 Aces, Faster Library Font Rendering Engine Computer & Information Sciences Font Technology Computer Science Graphite is a “smart font” system developed specifically to handle the complexities of lesser-known languages of the world.
Description Source: https://graphite.sil.org/
1. Support for creating 'smart fonts' with advanced typographic behavior
2. Capable of displaying writing systems with complex behaviors
3. Provides features such as contextual forms, ligatures, and reordering
4. Enables the creation of fonts for languages/scripts that require special typographic handling
Font Rendering, Typography, Smart Fonts https://graphite.sil.org/ https://graphite.sil.org/assets/resources/GDL.pdf https://graphite.sil.org/graide_tutorial Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.3.14
Faster: 1.3.14
Graphite is a system that can be used to create 'smart fonts' capable of displaying writing systems with various complex behaviors. Graphite fonts are capable of providing contextual forms, reordering, ligatures, and other advanced typographic behavior.
graphlan Anvil Graph Visualization Data Visualization Biological Sciences Graphlan is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Visualization Of Phylogenetic Trees, Annotation Of Trees With Metadata, Customizable Features For Tree Display, Support For Complex Tree Layouts, Interactive Viewing Capabilities Phylogenetics, Tree Visualization, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/graphlan Anvil: 1.1.3 Graphlan is a software tool used for the visualization and annotation of phylogenetic trees and their associated metadata. It allows users to create high-quality graphical representations of phylogenetic trees with customizable features and options.
graphmap Anvil Bioinformatics Tool Sequence Alignment Biological Sciences Genomics Graphmap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data. 1. Utilizes graphical FM index (GFM) for efficient read alignment
2. Designed for mapping large sets of short sequencing reads
3. Supports various next-generation sequencing data types
4. High performance and parallel processing capabilities
Alignment, Sequencing, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/graphmap Anvil: 0.6.3 GraphMap is a software tool for mapping next-generation sequencing data to a reference genome using the graphical FM index (GFM). It is designed to efficiently align large sets of short sequencing reads generated by modern high-throughput sequencing technologies.
graphviz Aces, Expanse, Faster Data Visualization Visualization Tool Computer & Information Sciences Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. Automatic Layout Algorithms For Visualization, Support For Various Input Formats Including Dot Language, Customizable Node Shapes, Colors, & Styles, Ability To Render Graphs In Various Output Formats Such As Png, Pdf, Svg Graph Visualization, Diagramming, Open Source Software Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.0.0
Expanse: Rsjj7Kb
Faster: 2.47.2, 2.50.0, 8.1.0
Graphviz is open source graph visualization software. It is used for creating structured diagrams such as flowcharts, network diagrams, and more.
graphviz-python Aces Visualization Tool Library Computer & Information Sciences Simple Python interface for Graphviz 1. Generate and customize graphs programmatically. 2. Render graphs in various formats such as PNG, PDF, SVG, etc. 3. Support for complex graph structures and layouts. Graph Visualization, Python Library, Network Analysis Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.20.1 graphviz-python is a Python library for creating and rendering graph visualizations using Graphviz. It provides a simple interface to create and manipulate graphs and visualize them in various formats.
grass Aces, Faster Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 8.2.0, 8.3.1
Faster: 8.2.0
greenlet Aces Programming Library Computer & Information Sciences greenlets are lightweight coroutines for in-process sequential concurrent programming.
Description Source: https://pypi.org/project/greenlet/
Efficient Micro-Threads (Coroutines), Concurrency Within A Single Process, Context Switching Between Greenlets, Simple Api For Implementing Coroutines Python Library, Concurrency, Coroutines https://github.com/python-greenlet/greenlet https://greenlet.readthedocs.io/en/latest/ https://greenlet.readthedocs.io/en/latest/greenlet.html
https://greenlet.readthedocs.io/en/latest/gui_example.html#gui-example
Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.0.2 Greenlet is a lightweight library that allows micro-threads to be utilized in a concurrent programming fashion within a single process. It provides a simple way to implement coroutines in Python.
gridss Anvil Tool Bioinformatics Biological Sciences Genomic Structural Variation Genetics Gridss is a module software suite containing tools useful for the detection of genomic rearrangements. 1. Structural variant calling from DNA sequencing data
2. Identification of complex, nested, and discontinuous structural variations
3. Detection of genomic rearrangements like insertions, deletions, inversions, and translocations
Structural Variant Calling, DNA Sequencing, Genomic Rearrangements Anvil: https://www.rcac.purdue.edu/software/gridss Anvil: 2.13.2 Gridss is a structural variant caller that identifies complex, nested, and discontinuous structural variations from high-throughput DNA sequencing data. It aims to improve the detection of genomic rearrangements, such as insertions, deletions, inversions, and translocations.
groff Aces, Faster Typesetting System Document Preparation System Computer & Information Sciences groff (GNU roff) is a typesetting system that reads plain text input files that include formatting commands to produce output in PostScript, PDF, HTML, or DVI formats or for display to a terminal. Formatting commands can be low-level typesetting primitives, macros from a supplied package, or user-defined macros. All three approaches can be combined.
Description Source: https://www.gnu.org/software/groff/
Typesetting System, Formatting Commands, Formatted Output, Unix Troff Implementation Typesetting, Text Formatting, Unix Utilities https://www.gnu.org/software/groff/ https://www.gnu.org/software/groff/manual/groff.html.node/index.html https://www.gnu.org/software/groff/manual/groff.html.node/Introduction.html
https://www.gnu.org/software/groff/manual/groff.html.node/Basics.html
https://www.systutorials.com/docs/linux/man/7-groff/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.22.4, 1.23.0
Faster: 1.22.4
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. It's a modern implementation of the classic Unix troff typesetting system.
gromacs Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Kyric, Ookami, Stampede3 Molecular Dynamics Software Simulation Software Biological Sciences Biophysics Chemistry GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers across the world. Efficient Algorithms For Molecular Dynamics Simulations, Optimized For Performance On Cpus, Gpus, & Other Accelerators, Support For Various Force Fields & Integrators, Analysis Tools For Processing Simulation Output Data, Extensive Community Support & Documentation Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems https://www.gromacs.org/ https://manual.gromacs.org/current/index.html https://tutorials.gromacs.org/
https://www.gromacs.org/workshop.html
https://www.gromacs.org/tutorial_webinar.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gromacs
Bridges-2: https://www.psc.edu/resources/software/gromacs
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2021.5-Cuda-11.4.1-Plumed-2.8.0, 2023.1-Cuda-11.7.0, 2023.1-Cuda-12.2.0, 2023.3-Cuda-11.8.0, ...
Anvil: 2020.2, 2021, 2021.2, 2021.3
Bridges-2: 2018, 2020.2-Cpu, 2020.4-Gpu
Delta: 2022.5.Cuda, 2022.5.X86_64
Expanse: Rspmhnj-Omp, Sbq2Qrc-Omp
Faster: 2020.5-Ramd-2.0, 2021-Constantph-2022.05.25, 2021, 2021.3, 2021.5-Cuda-11.4.1-Plumed-2.8.0, ...
Ookami: Gcc12.1/2022.3
Stampede-3: 2023.3, 2024
GROMACS (GROningen MAssive Parallel MD for Molecular Dynamics) is a versatile package for molecular dynamics simulations with a strong emphasis on high-performance computing capabilities.
grpc Faster Library/Framework Middleware Computer & Information Sciences, Software Engineering, Systems, & Development 1. Supports multiple programming languages such as C++, Java, Python, Go, etc.
2. Uses Protocol Buffers as the interface definition language for defining services and message types.
3. Bi-directional streaming, flow control, deadline propagation, and authentication are key features.
4. Supports synchronous and asynchronous programming models.
Rpc, Distributed Systems, Communication Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.44.0 gRPC is a high-performance, open-source remote procedure call (RPC) framework that enables client and server applications to communicate transparently, efficiently, and securely across distributed systems.
gsd-vmd Faster Other Natural Sciences 1. Visualization of simulation trajectories in the GSD file format.
2. Analysis of molecular simulation data.
3. Integration with VMD for advanced visualization capabilities.
4. Support for high-performance molecular simulation workflows.
Molecular Dynamics, Simulation Analysis, Trajectory Visualization Faster: https://hprc.tamu.edu/software/faster/ Faster: V0.4.0 GSD-VMD is a tool for visualizing and analyzing simulation trajectories stored in the GSD file format, a hierarchical file format built for high-performance molecular simulation workflows. It integrates with the popular VMD visualization software to provide a powerful toolset for molecular dynamics analysis.
gseapy Anvil Library Analysis Tool Biological Sciences Gene Expression Analysis Bioinformatics Gseapy is a python wrapper for GESA and Enrichr. Supports Gene Set Enrichment Analysis (Gsea), Offers Various Enrichment Analysis Methods, Allows Interpretation Of Gene Expression Data, Provides Tools For Pathway & Network Analysis Bioinformatics, Computational Biology, Python Library, Enrichment Analysis Anvil: https://www.rcac.purdue.edu/software/gseapy Anvil: 0.10.8 GSEApy is a Python library for Gene Set Enrichment Analysis (GSEA) and various enrichment analysis methods to interpret gene expression data.
gsl Aces, Anvil, Darwin, Delta, Expanse, Faster, Stampede3 Library Numerical Library Other Mathematics Mathematics The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. 1. Implementation of a comprehensive set of mathematical functions
2. High-performance numerical routines
3. Modular structure for easy integration into C and C++ applications
4. Extensive documentation and examples
5. Open-source and free to use
Numerical Library, Mathematical Functions, C Programming, C++ Programming https://www.gnu.org/software/gsl/ https://www.gnu.org/software/gsl/doc/html/index.html https://www.gnu.org/software/gsl/doc/html/usage.html
https://www.gnu.org/software/gsl/doc/html/err.html#examples
https://www.gnu.org/software/gsl/doc/html/linalg.html#examples
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gsl
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2.6, 2.7
Anvil: 2.4
Delta: 2.7.1
Expanse: Aji2Yx5, Gfpesxa, Ix3Kgnc, ...
Faster: 2.6, 2.7
Stampede-3: 2.7.1
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It provides a wide range of mathematical routines such as special functions, linear algebra, interpolation, numerical integration, random numbers, and more.
gslib Aces, Faster Geospatial Analysis Tool Library Earth & Environmental Sciences Geostatistics Geoscience A sparse communication library. gslib provides a wide range of geostatistical tools for variogram modeling, kriging, and spatial data analysis. It also includes utilities for data transformation and visualization of spatial data. Geostatistics, Fortran 77, Spatial Data, Variogram Modeling, Kriging Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.8
Faster: 1.0.8
gslib is an open-source and free collection of Fortran 77 subroutines for geostatistical applications.
gst-plugins-bad Aces, Faster Plugin Multimedia Computer & Information Sciences GStreamer Bad Plug-ins is a set of plug-ins that aren't up to par compared to the rest. They might be close to being good quality, but they're missing something - be it a good code review, some documentation, a set of tests, a real live maintainer, or some actual wide use.
Description Source: https://gstreamer.freedesktop.org/modules/gst-plugins-bad.html
1. Provides a variety of GStreamer plugins and elements.
2. Experimental plugins for testing new functionalities.
3. Plugins that are incomplete or lack proper testing.
4. Supplement to the GStreamer plugins base.
Multimedia, Plugin, Gstreamer https://gstreamer.freedesktop.org/modules/gst-plugins-bad.html https://gitlab.freedesktop.org/gstreamer/gstreamer/-/tree/main/subprojects/gst-plugins-bad/docs https://gstreamer.freedesktop.org/documentation/tutorials/basic/index.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/table-of-concepts.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/index.html?gi-language=c
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.20.2
Faster: 1.20.2
gst-plugins-bad is a collection of GStreamer plugins and elements that are not of high quality, experimental, or have not been tested well. These plugins are considered 'bad' due to various reasons such as being incomplete, breaking or lacking proper documentation.
gst-plugins-base Aces, Faster Plugin Library Computer & Information Sciences Multimedia Processing Computer Science GStreamer Base Plug-ins is a well-groomed and well-maintained collection of GStreamer plug-ins and elements, spanning the range of possible types of elements one would want to write for GStreamer. It also contains helper libraries and base classes useful for writing elements. A wide range of video and audio decoders, encoders, and filters are included.
Description Source: https://gstreamer.freedesktop.org/modules/gst-plugins-base.html
1. Support for various container formats like AVI, QuickTime, Matroska, etc.
2. Decoding and encoding support for a wide range of audio and video codecs.
3. Basic elements for audio and video playback, recording, streaming, and manipulation.
4. Integration with hardware-accelerated video decoding and encoding through VA-API, VDPAU, etc.
Audio Processing, Video Processing, Multimedia Framework https://gstreamer.freedesktop.org/modules/gst-plugins-base.html https://gitlab.freedesktop.org/gstreamer/gstreamer/-/tree/main/subprojects/gst-plugins-base/docs https://gstreamer.freedesktop.org/documentation/tutorials/basic/index.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/table-of-concepts.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/index.html?gi-language=c
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.18.5, 1.20.2, 1.22.1
Faster: 1.16.2, 1.18.4, 1.18.5, 1.20.2, 1.22.1
gst-plugins-base is a collection of GStreamer plugins and elements, which serve as the base for GStreamer. These plugins provide essential functionalities for building audio and video processing pipelines in GStreamer-based applications.
gstreamer Aces, Anvil, Faster Framework Media Processing Computer & Information Sciences GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
Description Source: https://gstreamer.freedesktop.org/
1. Support for a wide range of media formats and protocols. 2. Modular architecture that allows flexible construction of multimedia pipelines. 3. Extensive plugin architecture for additional features and format support. 4. Cross-platform compatibility. 5. Open-source and actively developed community. Multimedia, Framework, Media Processing, Audio, Video https://gstreamer.freedesktop.org/ https://gstreamer.freedesktop.org/documentation/ https://gstreamer.freedesktop.org/documentation/tutorials/basic/index.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/table-of-concepts.html?gi-language=c
https://gstreamer.freedesktop.org/documentation/tutorials/index.html?gi-language=c
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/gstreamer
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.18.5, 1.20.2, 1.22.1, 1.22.5
Anvil: 1.16.1
Faster: 1.16.2, 1.18.4, 1.18.5, 1.20.2, 1.22.1
GStreamer is a multimedia framework that allows the construction of graphs of media-handling components, ranging from simple Ogg/Vorbis playback to complex audio (mixing) and video (non-linear editing) processing. It is designed to be easily extended with new plugins that provide new functionality.
gtdbtk Anvil GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. Anvil: https://www.rcac.purdue.edu/software/gtdbtk Anvil: 1.7.0, 2.1.0
gthumb Delta Desktop Application Image Viewer/Editor Other Computer & Information Sciences Image Viewing & Browsing, Image Organization & Management, Basic Editing Functionalities, Slideshow Creation, Batch Processing Of Images Image Viewer, Image Browser, Image Management Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 3.12.0 gthumb is an image viewer and browser for the GNOME desktop environment. It also includes features for organizing and managing images.
gtk+ Faster Toolkit Application Software Computer & Information Sciences Cross-Platform Compatibility, Extensive Widget Library, Support For Numerous Programming Languages, Customizable Theming, Accessibility Features, Internationalization & Localization Support Gui Toolkit, Graphical User Interface, Desktop Application Development Faster: https://hprc.tamu.edu/software/faster/ Faster: 3.24.13, 3.24.23 GTK+ is a multi-platform toolkit for creating graphical user interfaces. It offers a comprehensive set of widgets for building GUIs and provides tools for interaction with the user interface. GTK+ is widely used in software development for creating desktop applications with a consistent look and feel across different operating systems.
gtk2 Aces, Faster Gui Toolkit Library Computer & Information Sciences Sciences Biology GTK is a widget toolkit. Each user interface created by GTK consists of UI elements known as widgets. The GTK programming interface is based on Object Orientation; widgets are organized in a hierarchy of classes—for instance, the window widget is also a specialised container, called a “bin”, that can hold at most one child widget. A window will be able to use functions that pertain to the widget, container, bin, and window classes.
Description Source: https://www.gtk.org/
1. Provides a set of graphical control elements
2. Supports event-driven programming
3. Easily customizable and themable
4. Allows for creating interactive and responsive GUIs
5. Cross-platform compatibility
Gui, Widget Toolkit, Cross-Platform https://www.gtk.org/ https://developer-old.gnome.org/gtk2/stable/index.html https://www.gtk.org/docs/getting-started/hello-world/
https://www.gtk.org/docs/getting-started/
https://www.gtk.org/docs/language-bindings/python/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.24.33
Faster: 2.24.33
GTK2 is a cross-platform widget toolkit for creating graphical user interfaces. It is used in a variety of applications to provide a user-friendly interface.
gtk3 Aces, Faster Development Toolkit Framework/Library Computer & Information Sciences Sciences Biology GTK is a widget toolkit. Each user interface created by GTK consists of UI elements known as widgets. The GTK programming interface is based on Object Orientation; widgets are organized in a hierarchy of classes—for instance, the window widget is also a specialised container, called a “bin”, that can hold at most one child widget. A window will be able to use functions that pertain to the widget, container, bin, and window classes.
Description Source: https://www.gtk.org/
Cross-Platform Compatibility, Extensive Widget Toolkit, Customizable Themes & Styles, Support For Various Programming Languages Gui Toolkit, Desktop Application Development, Cross-Platform Development, User Interface Design https://www.gtk.org/ https://docs.gtk.org/gtk3/ https://www.gtk.org/docs/getting-started/hello-world/
https://www.gtk.org/docs/getting-started/
https://www.gtk.org/docs/language-bindings/python/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.24.31, 3.24.35, 3.24.37
Faster: 3.24.31, 3.24.33, 3.24.35, 3.24.37
GTK3 is a widely-used toolkit for building graphical user interfaces and desktop applications. It provides a comprehensive set of tools and libraries for creating interactive and visually appealing applications across multiple platforms.
gtk4 Aces, Faster Development Tool Graphical User Interface (Gui) Toolkit Computer & Information Sciences Sciences Biology GTK is a widget toolkit. Each user interface created by GTK consists of UI elements known as widgets. The GTK programming interface is based on Object Orientation; widgets are organized in a hierarchy of classes—for instance, the window widget is also a specialised container, called a “bin”, that can hold at most one child widget. A window will be able to use functions that pertain to the widget, container, bin, and window classes.
Description Source: https://www.gtk.org/
Cross-Platform Support, Customizable Themes & Styling, Support For Various Programming Languages, Integration With Popular Programming Languages & Development Environments Gui Toolkit, Cross-Platform Development, User Interface Design https://www.gtk.org/ https://docs.gtk.org/gtk4/ https://www.gtk.org/docs/getting-started/hello-world/
https://www.gtk.org/docs/getting-started/
https://www.gtk.org/docs/language-bindings/python/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.7.0
Faster: 4.7.0
GTK4 is a multi-platform toolkit for creating graphical user interfaces. It is used for developing applications with a consistent look and feel across different operating systems.
gts Aces, Faster Computational Software Library Computer & Information Sciences The GNU Triangulated Surface Library (GTS) is a library for constructing and manipulating surface meshes, particularly 3D triangulated surfaces. It offers data structures and algorithms for tasks like mesh simplification, refinement, and more. Computation Of Geometric Surface Properties, Triangulation Of Complex Surfaces, Support For 2D & 3D Geometric Data Structures, Mesh Generation & Manipulation Tools Computational Geometry, Surface Properties, Mesh Generation https://gts.sourceforge.net/ https://gts.sourceforge.net/reference/book1.html https://github.com/lsaavedr/gts/tree/master/examples
https://gts.sourceforge.net/samples.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.7.6
Faster: 0.7.6
GNU Triangulated Surface Library (GTS) is a free library for computational geometry. It includes many useful functions for calculating surface properties and constructing complex surfaces using triangulations.
gubbins Anvil Biological Sciences Bioinformatics Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. 1. Detection of recombination events in bacterial populations
2. Analysis of whole-genome sequence data
3. Identification of genomic regions under recombination
4. Visualization of recombination events
5. Phylogenetic tree construction
Bacterial Recombination, Whole-Genome Sequencing, Population Genetics Anvil: https://www.rcac.purdue.edu/software/gubbins Anvil: 3.2.0, 3.3 Gubbins is a software tool for the analysis of bacterial recombination data. It identifies recombination events in bacterial populations from whole-genome sequence data.
guile Aces, Faster Interpreter Programming Language Computer & Information Sciences Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. Guile offers a powerful Scheme interpreter, a reliable extension language for C and C++ programs, an interactive environment for Scheme development, a large standard library, and a module system that supports extension scripts and plugins. Programming Language, Scripting Language, Embeddable, Customizable Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.0.7
Faster: 1.8.8, 3.0.7
Guile is an implementation of the Scheme programming language, providing a flexible and embeddable scripting environment for applications. It aims to be a platform for creating applications and libraries that require customizations and extensibility.
guppy Anvil, Bridges-2 Basecaller Bioinformatics Tool Biological Sciences Next-Generation Sequencing Genomics Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' production basecalling algorithms and several bioinformatic post-processing features. It is run from the command line in Windows, Mac OS, and on multiple Linux platforms. Guppy is also integrated with our sequencing instrument software, MinKNOW, and a subset of Guppy features are available via the MinKNOW UI. A selection of configuration files allows basecalling of DNA and RNA libraries made with Oxford Nanopore Technologies’ current sequencing kits, in a range of flow cells.
Description Source: https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview
Basecalling Of Raw Electrical Signal Data From Nanopore Sequencing Devices, Conversion Of Raw Signal Data Into Nucleotide Sequences, Support For Real-Time Basecalling During Sequencing Runs, Integration With Oxford Nanopore Technologies' Sequencing Platforms, Compatibility With Various Sequencing Protocols Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/expert-settings https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/setting-up-a-run-configurations-and-parameters Anvil: https://www.rcac.purdue.edu/software/guppy
Bridges-2: https://www.psc.edu/resources/software/guppy
Anvil: 6.0.1, 6.5.7
Bridges-2: 6.0.0, 6.5.7
Guppy is a basecaller developed by Oxford Nanopore Technologies for processing raw electrical signal data generated by their nanopore sequencing devices. It is designed to convert the raw signal data into nucleotide sequences, providing a platform for downstream analysis in genomics research.
guppy-gpu Bridges-2 Bioinformatics Tool Analysis Tool Biological Sciences Genetics Bioinformatics 1. Utilizes GPU acceleration for rapid basecalling
2. Optimized for Oxford Nanopore sequencing data
3. Supports real-time sequencing data analysis
4. Provides high-throughput processing capabilities
Basecaller, Oxford Nanopore, Sequencing, Gpu Acceleration Bridges-2: https://www.psc.edu/resources/software/guppy-gpu Bridges-2: 6.0.1 Guppy is a basecaller software for Oxford Nanopore sequencing data. The GPU version utilizes the power of graphics processing units to accelerate the basecalling process for faster and more efficient analysis of sequencing data.
gurobi Anvil, Bridges-2, Delta Solver Optimization Software Mathematics Gurobi optimizer is a solver for mathematical programming thhat includes a linear programming solver, a mixed-integer linear programming solver, a mixed-integer quadratic programming solver, a quadratic programming solver, a quadratically constrained programming solver, and a mixed-integer quadratically constrained programming solver.
Description Source: https://www.gurobi.com/solutions/gurobi-optimizer/
Some core features of Gurobi include advanced performance (fast and scalable algorithms), support for a variety of programming languages (Python, MATLAB, C++, etc.), ability to handle complex optimization models, interactive visualizations, and extensive documentation and user support. Optimization, Mathematical Programming, Linear Programming, Mixed-Integer Programming https://www.gurobi.com/ https://www.gurobi.com/documentation/ https://www.gurobi.com/documentation/current/examples/index.html
https://support.gurobi.com/hc/en-us/articles/13444017491857-How-do-I-use-the-Gurobi-Command-Line-Interface-gurobi-cl
https://support.gurobi.com/hc/en-us/articles/14165975461393-Tutorials-Getting-Started-with-the-Gurobi-APIs
Anvil: https://www.rcac.purdue.edu/software/gurobi
Bridges-2: https://www.psc.edu/resources/software/gurobi
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Anvil: 9.5.1
Bridges-2: 9.1.1, 9.5.0
Delta: 10.0.1
Gurobi Optimization is a high-performance mathematical programming solver for linear programming (LP), mixed-integer programming (MIP), and other related optimization problems.
gurobi-dev Delta Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 10.0.3
gymnasium Faster Programming Library Library Mathematics Applied Computer Science Computer Science 1. Allows users to create and manipulate mathematical expressions
2. Supports complex mathematical operations and transformations
3. Provides a simple and intuitive interface for working with mathematical equations
4. Compatible with Python programming language
5. Useful for symbolic mathematics and equation handling tasks
Python Library, Mathematical Expressions, Equation Manipulation Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.26.3 Gymnasium is a Python library which provides tools and utilities for creating and manipulating complex mathematical expressions and equations.
gzip Aces, Faster Compression Tool Utility Engineering & Technology gzip is a single-file/stream lossless data compression utility, where the resulting compressed file generally has the suffix .gz. gzip also refers to the associated compressed data format used by the utility.
Description Source: https://www.gzip.org/
Compression and decompression of files, support for various compression levels, integration with tar for creating compressed archives, fast and efficient compression algorithms. File Compression, Data Storage, Data Transfer https://www.gnu.org/software/gzip/ https://www.gnu.org/software/gzip/manual/gzip.html https://www.gnu.org/software/gzip/manual/gzip.html#Sample
https://www.gnu.org/software/gzip/manual/gzip.html#Invoking-gzip
https://www.youtube.com/watch?v=NLtt4S9ErIA
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.10, 1.12
Faster: 1.10, 1.12
gzip is a file compression and decompression tool used to reduce the size of files for storage or transfer purposes. It is a widely used compression utility in Unix-like operating systems.
h5py Aces, Faster Library Python Library Computer & Information Sciences The h5py package is a Pythonic interface to the HDF5 binary data format. It lets you store huge amounts of numerical data, and easily manipulate that data from NumPy. For example, you can slice into multi-terabyte datasets stored on disk, as if they were real NumPy arrays. Thousands of datasets can be stored in a single file, categorized and tagged however you want.
Description Source: https://www.h5py.org/
High-Level Interface To The Hdf5 Library, Efficiently Store & Manipulate Large Numerical Datasets, Seamless Integration With Numpy Arrays, Support For Complex Data Structures, Ability To Access Data Stored In Hdf5 Files Python Library, Data Storage, Numerical Data, Data Manipulation https://www.h5py.org/ https://docs.h5py.org/en/stable/ https://docs.h5py.org/en/stable/quick.html#core-concepts
https://docs.h5py.org/en/stable/high/file.html#opening-creating-files
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.1.0, 3.2.1, 3.6.0, 3.7.0, 3.8.0, 3.9.0, 3.10.0
Faster: 2.10.0-Python-3.7.4, 2.10.0-Python-3.8.2, 3.1.0, 3.2.1, 3.6.0, 3.7.0, 3.8.0
h5py is a Python library providing a high-level interface to the HDF5 library. It allows you to store huge amounts of numerical data and easily manipulate that data from NumPy.
hadoop Anvil, Expanse Framework Data Processing Computer & Information Sciences The Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models. It is designed to scale up from single servers to thousands of machines, each offering local computation and storage. Rather than rely on hardware to deliver high-availability, the library itself is designed to detect and handle failures at the application layer, so delivering a highly-available service on top of a cluster of computers, each of which may be prone to failures.
Description Source: https://hadoop.apache.org/
Distributed Storage, Distributed Processing, Fault Tolerance, Scalability, Flexibility, High Availability Big Data, Data Processing, Distributed Computing https://hadoop.apache.org/ https://apache.github.io/hadoop/ https://hadoop.apache.org/docs/current/hadoop-project-dist/hadoop-common/UnixShellGuide.html
https://hadoop.apache.org/docs/current/hadoop-project-dist/hadoop-hdfs/HdfsUserGuide.html
https://www.tutorialspoint.com/hadoop/index.htm
Anvil: https://www.rcac.purdue.edu/software/hadoop
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 3.3.0
Expanse: Bfyu354
Hadoop is an open-source framework used for distributed storage and processing of large sets of data on computer clusters using simple programming models.
hail Anvil Analysis Tool Bioinformatics & Computational Biology Biological Sciences Hail is an open-source, general-purpose, Python-based data analysis tool with additional data types and methods for working with genomic data. Scalable Genetic Analysis Platform, Storage & Processing Of Large-Scale Genetic Data, Exploration, Analysis, & Visualization Of Genomic Data, Support For High-Throughput Sequencing Data, Integration With Apache Spark For Distributed Computing Genetic Analysis, Genomics, Big Data, Bioinformatics, Genetic Data Analysis Anvil: https://www.rcac.purdue.edu/software/hail Anvil: 0.2.94, 0.2.98 Hail is an open-source, scalable genetic analysis platform built to store and process large-scale genetic data with ease. It is tailored for exploring, analyzing, and visualizing genomic data on research scale.
hap.py Anvil Bioinformatics Tool Computational Tool Biological Sciences Hap.py is a tool to compare diploid genotypes at haplotype level. It provides a variety of metrics for evaluating variant calls, such as precision, recall, F1 score, sensitivity, specificity, and more. It supports VCF and BED files as input and generates detailed reports to aid in interpreting the accuracy of variant calls. Variant Calling, Sequencing, Genomics Anvil: https://www.rcac.purdue.edu/software/hap.py Anvil: 0.3.9 hap.py is a toolkit for assessing the accuracy of variants (SNPs, indels, and block substitutions) detected by various sequencing technologies, including data from whole-genome sequencing, whole-exome sequencing, and targeted gene panels.
harfbuzz Aces, Faster, Ookami Library Package Computer & Information Sciences HarfBuzz is a text shaping library. Using the HarfBuzz library allows programs to convert a sequence of Unicode input into properly formatted and positioned glyph output—for any writing system and language.
Description Source: https://harfbuzz.github.io/
Unicode text shaping, support for complex scripts, language-specific shaping rules, high-quality text layout, customization options for font features, text rendering optimization. Text Shaping Engine, Unicode Text, Text Layout, Font Features Customization https://github.com/harfbuzz/harfbuzz https://harfbuzz.github.io/ https://harfbuzz.github.io/getting-started.html
https://harfbuzz.github.io/a-simple-shaping-example.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.8.1, 2.8.2, 4.2.1, 5.3.1
Faster: 2.6.4, 2.6.7, 2.8.1, 2.8.2, 4.2.1, 5.3.1
Ookami: 8.3.0
HarfBuzz is an open-source text shaping engine. It is used to convert Unicode text to beautifully formatted and language-appropriate glyphs. HarfBuzz focuses on providing correct script shaping for complex scripts and languages.
hashdeep Bridges-2 Hashing Utility Computer & Information Sciences hashdeep is a program to compute, match, and audit hashsets. With traditional matching, programs report if an input file matched one in a set of knows or if the input file did not match. It's hard to get a complete sense of the state of the input files compared to the set of knowns. It's possible to have matched files, missing files, files that have moved in the set, and to find new files not in the set. Hashdeep can report all of these conditions. It can even spot hash collisions, when an input file matches a known file in one hash algorithm but not in others. The results are displayed in an audit report.
Description Source: https://md5deep.sourceforge.net/
The tool supports multiple hashing algorithms such as MD5, SHA-1, SHA-256, SHA-384, SHA-512, and many others. It can recursively compute hashes for files in a directory structure, output the results in various formats, and verify file integrity by comparing hashes. Hashing, Data Integrity, Security https://github.com/jessek/hashdeep https://md5deep.sourceforge.net/hashdeep.html https://md5deep.sourceforge.net/start-hashdeep.html
https://github.com/jessek/hashdeep/blob/master/doc/start-hashdeep.html
Bridges-2: https://www.psc.edu/resources/software/hashdeep Bridges-2: 4.4 hashdeep is a cross-platform hashing utility that calculates and verifies hash signatures for files and directories.
hatchling Aces, Faster Research Tool Simulation & Modeling Biological Sciences Population Dynamics Of Early Life Stages Environmental Biology Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager. Population Dynamics Modeling, Simulation Of Early Life Stages Of Organisms, Analysis Of Environmental Factors On Hatchling Survival & Growth, Ecological Study Support Population Dynamics, Ecology, Simulation, Environmental Factors Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.18.0
Faster: 1.11.1, 1.18.0
Hatchling is a software tool designed for simulating and analyzing population dynamics in ecological studies, particularly focusing on early life stages of organisms such as fish, amphibians, and invertebrates. It allows researchers to model various environmental factors affecting the survival and growth of hatchlings in different ecosystems.
hdbscan Faster Data Mining Tool Clustering Algorithm Computer & Information Sciences Density-Based Clustering, Automatic Cluster Determination, Ability To Handle Noise/Outliers, Scalable To Large Datasets, Robust To Different Cluster Geometries & Densities Clustering Algorithm, Data Mining, Unsupervised Learning, Machine Learning Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.8.27 HDBSCAN (Hierarchical Density-Based Spatial Clustering of Applications with Noise) is a clustering algorithm that is based on density rather than distance, and in contrast to many other clustering algorithms, HDBSCAN has a parameterless approach that automatically determines the number of clusters in the data.
hdf Aces, Anvil, Expanse, Faster File Format Data Management & Storage Other Computer & Information Sciences Hierarchical Data Format (HDF) refers to a versatile file format commonly used to store and manage large volumes of complex data, such as scientific datasets and images. It provides a standardized and efficient way for organizing and sharing data. Supports Large, Complex, & Multidimensional Datasets, Allows For Efficient Data Organization & Storage, Provides Tools For Data Management, Manipulation, & Visualization, Offers Apis For Different Programming Languages Such As C, Python, & Java Data Management, File Format, Data Visualization, Api https://portal.hdfgroup.org/hdf4/ https://portal.hdfgroup.org/documentation/hdf4-docs/HDF4_Reference_Manual.pdf https://portal.hdfgroup.org/documentation/hdf4-docs/HDF4_Users_Guide.pdf Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/hdf
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 4.2.15, 4.2.16-2
Anvil: 4.2.15
Expanse: 4.2.15
Faster: 4.2.15, 4.2.16-2
HDF (Hierarchical Data Format) is a flexible and extensible file format for storing and managing large amounts of data. It supports various data types, attributes, and metadata, making it suitable for a wide range of scientific and engineering applications.
hdf-eos Aces Library Computational Software Physical Sciences Atmospheric Sciences Earth & Environmental Sciences HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. 1. Provides tools for managing and processing Earth science data.
2. Supports a wide range of data formats and metadata.
3. Includes libraries for data visualization, extraction, and manipulation.
4. Optimized for handling large volumes of geospatial data.
5. Designed specifically for the storage and retrieval of Earth science data.
Data Management, Data Processing, Earth Science, Geospatial Data Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.20 HDF-EOS (Hierarchical Data Format - Earth Observing System) is a software library developed by NASA for managing and processing Earth science data in the HDF (Hierarchical Data Format) format.
hdf-eos5 Aces Data Management & Analysis Library Natural Sciences Atmospheric Sciences Earth & Environmental Sciences HDF-EOS libraries are software libraries built on HDF libraries. It supports three data structures for remote sensing data: Grid, Point and Swath. 1. Tools for reading, writing, and manipulating HDF5 files
2. Support for EOS data structures and metadata
3. APIs for accessing and processing EOS datasets
4. Integration with popular programming languages like C, Fortran, and Python
5. Visualization capabilities for Earth science data
Nasa, Earth Observing System, Data Management, Data Analysis, Hdf5 Format Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.16 HDF-EOS5 is a software library developed by NASA that provides tools and interfaces for working with EOS (Earth Observing System) data in the Hierarchical Data Format (HDF5) format. It is specifically designed for the management and analysis of Earth science data collected by various NASA missions.
hdf4 Darwin Library Data Management Computer & Information Sciences 1. Support for various data types and structures
2. High-performance I/O operations
3. Scalable and flexible data storage
4. Tools for data visualization and manipulation
5. Support for parallel and distributed computing
6. Cross-platform compatibility
Data Management, I/O Operations, Data Storage, Data Visualization, Parallel Computing Hierarchical Data Format Version 4 (HDF4) is a data management software library and file format that provides high-performance I/O capabilities for storing and managing large and complex data. HDF4 is designed to support diverse data types and structures, enabling efficient data storage, retrieval, and sharing.
hdf5 Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Ookami, Stampede3 Library/Tool Data Management Other Computer & Information Sciences HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data Support For Various Data Types & Structures, Hierarchical Organization Of Data, High-Performance I/O Capabilities, Parallel I/O For Large-Scale Data Processing, Data Compression & Chunking For Efficient Storage, Cross-Platform Compatibility, Support For Metadata & Attributes, Integration With Other Programming Languages Like Python, C, & Fortran File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing https://www.hdfgroup.org/solutions/hdf5/ https://docs.hdfgroup.org/hdf5/develop/ https://docs.hdfgroup.org/hdf5/develop/_getting_started.html
https://docs.hdfgroup.org/hdf5/develop/_u_g.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/hdf5
Bridges-2: https://www.psc.edu/resources/software/hdf5
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 1.10.7, 1.12.1, 1.12.2, 1.14.0, 1.14.2, 1.14.3
Anvil: 1.10.7
Bridges-2: 1.10.7-Gcc10.2.0, 1.12.0-Intel20.4
Delta: 1.14.3
Expanse: Butdr5C, E27Q55Q, ...
Faster: 1.10.2, 1.10.5, 1.10.6, 1.10.7, 1.12.1, 1.12.2, 1.13.1, 1.14.0, 1.14.3
Ookami: Parallel/Openmpi/Llvm14/1.12.1
Stampede-3: 1.10.11, 1.14.0, 1.14.3
HDF5 (Hierarchical Data Format version 5) is a file format and a suite of tools developed by the HDF Group for managing and storing large and complex data. It is designed to store and organize large amounts of data efficiently, enabling fast data access and sharing.
helen Anvil Tools Bioinformatics Biological Sciences Genetics Biophysics HELEN is a multi-task RNN polisher which operates on images produced by MarginPolish. Helen offers various features including the ability to perform differential analysis of epigenetic marks, identify enriched regions of histone modifications, visualize genomic annotations, and integrate multiple types of epigenomic data for comprehensive analysis. Genomic Analysis, Epigenomics, High-Throughput Sequencing, DNA Modifications, Chromatin Structure Anvil: https://www.rcac.purdue.edu/software/helen Anvil: 1.0 Helen is a software tool for analyzing genomic and epigenomic annotations from large-scale sequencing data. It is designed to extract biological insights from high-throughput sequencing data related to DNA modifications and chromatin structure.
help2man Aces, Faster Utility Documentation Tool Engineering & Technology Software Development Software Engineering, Systems, & Development help2man is a tool for automatically generating simple manual pages from program output.
Description Source: https://www.gnu.org/software/help2man/#Overview
help2man automates the generation of manual pages for programs that lack a man page but provide a '--help' or '--version' option. It extracts the necessary information from these options and formats them into a manual page. Documentation, Man Pages, Automation https://www.gnu.org/software/help2man/ https://www.gnu.org/software/help2man/ https://www.gnu.org/software/help2man/help2man.html#Example Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.47.8, 1.47.16, 1.48.3, 1.49.2, 1.49.3
Faster: 1.47.4, 1.47.7, 1.47.8, 1.47.10, 1.47.12, 1.47.16, 1.48.3, 1.49.2, 1.49.3
help2man is a tool that can generate simple man pages from the '--help' and '--version' output of other commands.
hh-suite Aces, Faster Computational Software Bioinformatics Biological Sciences HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous proteins.
Description Source: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7
1. Sensitive protein sequence searching using profile hidden Markov models. 2. Alignment of protein sequences. 3. Detection of remote homologs. 4. Prediction of protein structures. Protein Sequence Searching, Profile Hidden Markov Models, Protein Structure Prediction https://github.com/soedinglab/hh-suite https://github.com/soedinglab/hh-suite/wiki#summary-of-command-line-parameters https://github.com/soedinglab/hh-suite/wiki#brief-tutorial-to-hhsuite-tools Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.0
Faster: 3.3.0
HH-suite is a software package for sensitive protein sequence searching based on profile hidden Markov models. It includes tools for the alignment of protein sequences, detecting remote homologs, and predicting protein structures.
hic-pro Anvil Data Analysis Bioinformatics Tool Biological Sciences Chromatin Structure & Function Genomics Hicpro is an optimized and flexible pipeline for Hi-C data processing. Preprocessing Raw Hi-C Data, Mapping Reads To The Reference Genome, Filtering & Processing Valid Interaction Pairs, Normalization & Visualization Of Interactions, Quality Control Assessment Of Hi-C Data, Identifying Topological Domains & Chromatin Interactions Bioinformatics, Genomics, Chromatin Structure, Hi-C Data, Data Visualization, Chromatin Interactions Anvil: https://www.rcac.purdue.edu/software/hic-pro Anvil: 3.0.0, 3.1.0 HiC-Pro is a bioinformatics pipeline for processing, analyzing, and visualizing high-throughput chromatin conformation capture (Hi-C) data. It allows users to generate significant biological insights by studying chromatin structure, genome organization, and 3D chromatin interactions.
hicexplorer Anvil Bioinformatics Data Analysis Biological Sciences Chromatin Structure Genomics Hicexplorer is a set of tools to process, normalize and visualize Hi-C data. Processing & Normalization Of Hi-C Data, Identification Of Topologically Associated Domains (Tads), Visualization Of Hi-C Contact Matrices, Detection Of Chromatin Loops, Analysis Of Interaction Frequencies Between Genomic Regions Hi-C Data Analysis, Genome 3D Organization, Genomics Anvil: https://www.rcac.purdue.edu/software/hicexplorer Anvil: 3.7.2 HicExplorer is a software package designed for the analysis, visualization, and interpretation of Hi-C data, which is used to study the 3D organization of the genome.
hifiasm Anvil, Faster Bioinformatics Genome Assembly Biological Sciences Genetics Biological Sciences Hifiasm is fast haplotype-resolved de novo assembler for PacBio HiFi reads. Haplotype-Resolved De Novo Assembly, Supports Pacbio Hifi Reads, Fast & Scalable Assembler, De Novo Assembly Anvil: https://www.rcac.purdue.edu/software/hifiasm
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 0.16.0, 0.18.5
Faster: 0.19.4-R575
Hifiasm is a fast and scalable haplotype-resolved de novo assembler for PacBio HiFi reads.
highway Aces, Faster Statistical Tool Data Analysis Biological Sciences Genetics Bioinformatics Highway is a C++ library that provides portable SIMD/vector intrinsics.
Description Source: https://github.com/google/highway
Identification Of Driver Genes & Pathways In Cancer, Analysis Of Somatic Mutations, Processing Of Tumor Samples Bioinformatics, Computational Biology, Statistical Analysis https://github.com/google/highway https://google.github.io/highway/en/master/ https://google.github.io/highway/en/master/README.html#examples
https://google.github.io/highway/en/master/README.html#quick-start
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.3, 1.0.4
Faster: 1.0.3, 1.0.4
HighWay is an open-source statistical software tool designed for the identification of driver genes and pathways in cancer based on the analysis of somatic mutations across a cohort of tumor samples.
hipify-clang Faster Code Translation Tool Compiler Computer & Information Sciences 1. Translates CUDA source code to HIP source code.
2. Facilitates the migration of CUDA applications to AMD GPUs.
3. Helps in leveraging the performance of AMD GPUs for existing CUDA projects.
Cuda, Hip, Gpu Computing, Code Translation Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.2.0 hipify-clang is a tool that translates CUDA code to HIP (Heterogeneous-Compute Interface for Portability) code, enabling the porting of CUDA applications to AMD GPUs.
hipsycl Faster Programming Library Compiler Computer & Information Sciences Parallel & Distributed Computing Computer Science 1. Support for SYCL, a single-source standard for heterogeneous parallel programming. 2. Targeting CPUs, CUDA, and HIP backends for flexibility in hardware support. 3. Portable performance across different hardware platforms. 4. Integration with various development environments and tools for ease of use. Heterogeneous Computing, Parallel Programming, Hardware Acceleration Faster: https://hprc.tamu.edu/software/faster/ Faster: 0.9.3 hipsycl is a SYCL implementation targeting CPUs, CUDA, and HIP backends for heterogeneous systems, allowing for portable performance across different hardware platforms.
hiredis Aces, Faster Library Client Library Computer & Information Sciences Hiredis is a minimalistic C client library for the Redis database.
Description Source: https://github.com/redis/hiredis
1. Support for connecting to Redis servers
2. Commands to execute Redis commands like SET, GET, INCR, etc.
3. Asynchronous operation support
4. Pipelining support for performing multiple commands in a single round trip
Redis, Database, C Library https://redis.io/lp/hiredis/ https://github.com/redis/hiredis https://github.com/redis/hiredis/blob/master/examples/example.c
https://github.com/redis/hiredis/tree/master/examples
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.0.2
Faster: 1.0.2
Hiredis is a minimalistic C client library for the Redis database, offering a simple interface to interact with Redis servers from C-based applications. It aims to maintain an API that is both high-performance and easy to use, providing basic functionality to communicate with Redis servers.
hisat2 Aces, Anvil, Bridges-2, Expanse, Faster Alignment Tool Bioinformatics Biological Sciences Sciences Biology HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. Based on an extension of BWT for graphs (Sirén et al. 2014), we designed and implemented a graph FM index (GFM), an original approach and its first implementation. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM).
Description Source: https://daehwankimlab.github.io/hisat2/
Fast & Sensitive Alignment Of Ngs Reads, Mapping Of DNA & RNA Reads, Alignment Against General Human Population Or A Single Reference Genome, Improved Performance & New Capabilities Compared To Hisat & Bowtie Alignment, Ngs, Genomics, Transcriptomics https://daehwankimlab.github.io/hisat2/ https://daehwankimlab.github.io/hisat2/manual/ https://daehwankimlab.github.io/hisat2/howto/ . https://daehwankimlab.github.io/hisat2/manual/#getting-started-with-hisat2
https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-reads-to-counts/tutorial.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/hisat2
Bridges-2: https://www.psc.edu/resources/software/hisat2
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.2.1
Anvil: 2.2.1
Bridges-2: 2.2.1
Expanse: Qip6Jby
Faster: 2.2.1
HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). It builds on HISAT and Bowtie, allowing for significantly improved performance and new capabilities.
hmmer Aces, Anvil, Bridges-2, Faster Bioinformatics Tool Analysis Tool Biological Sciences Proteomics Bioinformatics HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Description Source: http://hmmer.org/
Protein Sequence Analysis, Profile Hidden Markov Models (Hmms), Homology Search, Conserved Protein Domain Identification, Sequence Annotation Bioinformatics, Computational Biology, Proteomics, Sequence Analysis http://hmmer.org/ http://hmmer.org/documentation.html http://eddylab.org/software/hmmer/Userguide.pdf
https://github.com/EddyRivasLab/hmmer/blob/master/documentation/userguide/tutorial.tex
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/hmmer
Bridges-2: https://www.psc.edu/resources/software/hmmer
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.2
Anvil: 3.3.2
Bridges-2: 3.3.1
Faster: 3.3.2
Hmmer is a software suite used for protein sequence analysis based on profile hidden Markov models (HMMs). It is widely used for searching sequence databases for homologs of protein sequences, identifying conserved protein domains, and annotating protein sequences based on sequence alignment.
homer Anvil, Bridges-2 Tool Computational Biology Biological Sciences Bioinformatics Genetics HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment.
Description Source: http://homer.ucsd.edu/homer/motif/
1. Motif discovery in DNA sequences. 2. Identification of transcription factor binding sites. 3. Next-generation sequencing data analysis. 4. De novo motif discovery. 5. Integration with various genomic databases. Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites http://homer.ucsd.edu/homer/ http://homer.ucsd.edu/homer/introduction/programs.html http://homer.ucsd.edu/homer/basicTutorial/index.html
http://homer.ucsd.edu/homer/motif/index.html
Anvil: https://www.rcac.purdue.edu/software/homer
Bridges-2: https://www.psc.edu/resources/software/homer
Anvil: 4.11
Bridges-2: 4.11.0
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for motif discovery and next-gen sequencing analysis. It is widely used for identifying transcription factor binding sites and novel motifs in DNA sequences.
homopolish Anvil Genome Assembly Tool Bioinformatics Tool Biological Sciences Genomics Bioinformatics Homopolish is a genome polisher originally developed for Nanopore and subsequently extended for PacBio CLR. Error Correction Of Long-Read Assemblies Using Short Reads, Improving The Accuracy Of Genome Assemblies, Facilitates The Generation Of High-Quality Genome Assemblies Bioinformatics, Genome Assembly, Error Correction, Long Reads, Short Reads Anvil: https://www.rcac.purdue.edu/software/homopolish Anvil: 0.4.1 Homopolish is a tool for polishing long-read assemblies using shorter reads. It takes long reads from a genome assembly and error-corrects them using short reads to produce a more accurate assembly.
horovod Aces, Faster Library/Framework Distributed Deep Learning Training Framework Computer & Information Sciences Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.
Description Source: https://horovod.ai/
Horovod supports training deep learning models on multiple GPUs across multiple nodes, providing fast and efficient distributed training. It is designed to be easy to use and integrates seamlessly with popular deep learning frameworks such as TensorFlow, Keras, PyTorch, and MXNet. Horovod incorporates optimizations for reducing communication overhead and achieving high performance on large-scale distributed systems. Deep Learning, Distributed Training, Machine Learning, Gpu Acceleration, High Performance Computing https://horovod.ai/ https://horovod.readthedocs.io/en/stable/ https://horovod.ai/getting-started/
https://horovod.readthedocs.io/en/stable/summary_include.html#usage
https://horovod.readthedocs.io/en/stable/summary_include.html#guides
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.22.1-Cuda-11.3.1-Tensorflow-2.6.0, 0.28.1-Cuda-11.7.0-Tensorflow-2.11.0, 0.28.1-Cuda-11.7.0-Pytorch-1.12.1
Faster: 0.18.2-Tensorflow-1.15.2-Python-3.7.4, 0.22.0-Pytorch-1.8.1, 0.22.1-Cuda-11.3.1-Tensorflow-2.6.0, 0.23.0-Tensorflow-2.5.0, ...
Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and MXNet. It significantly improves the speed and scale of distributed deep learning training.
hossedu Faster Teaching & Learning Tool Educational Software Computer & Information Sciences Computer Science This software provides interactive lessons, coding exercises, quizzes, and tutorials to help students understand concepts such as data structures, algorithms, programming languages, and software development. Educational Software, Computer Science, Programming Faster: https://hprc.tamu.edu/software/faster/ Faster: 2018 HOSSedu is an educational software tool designed for teaching and learning in the field of computer science and programming.
how_are_we_stranded_here Anvil How_are_we_stranded_here is a python package for testing strandedness of RNA-Seq fastq files. Anvil: https://www.rcac.purdue.edu/software/how_are_we_stranded_here Anvil: 1.0.1
hpc toolkit Jetstream Toolkit Performance Analysis Tools Engineering & Technology HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.
Description Source: http://hpctoolkit.org/
Performance Analysis, Debugging Support, Profiling Capabilities, Parallel Code Optimization, Visualization Of Performance Data Hpc, Performance Analysis, Parallel Computing, Optimization, Debugging http://hpctoolkit.org/ http://hpctoolkit.org/documentation.html http://hpctoolkit.org/manual/HPCToolkit-users-manual.pdf
http://hpctoolkit.org/training.html
HPC Toolkit is a collection of tools designed to assist users in optimizing and analyzing the performance of their parallel scientific applications on high-performance computing (HPC) systems.
hpc-x Aces Hpc Tools Tools & Libraries Engineering & Technology NVIDIA HPC-X is a comprehensive software package that includes Message Passing Interface (MPI), Symmetrical Hierarchical Memory (SHMEM) and Partitioned Global Address Space (PGAS) communications libraries, and various acceleration packages. hpc-x includes optimized libraries and tools for parallel computing, high-performance compilers, performance analysis tools, and debugging utilities. It provides support for distributed memory parallel computing using MPI (Message Passing Interface) and shared memory parallel computing using OpenMP. Hpc, High-Performance Computing, Scientific Computing, Parallel Computing Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.14 hpc-x is a high-performance computing (HPC) software package designed to provide optimized libraries, tools, and compilers for scientific computing on HPC systems. It aims to enhance the performance and efficiency of parallel computing applications on modern HPC architectures.
hpctoolkit Anvil HPCToolkit is an integrated suite of tools for measurement and analysis of program performance on computers ranging from multicore desktop systems to the nation's largest supercomputers. By using statistical sampling of timers and hardware performance counters, HPCToolkit collects accurate measurements of a program's work, resource consumption, and inefficiency and attributes them to the full calling context in which they occur.
Description Source: http://hpctoolkit.org/
http://www.hpctoolkit.org/ http://hpctoolkit.org/documentation.html http://hpctoolkit.org/manual/HPCToolkit-users-manual.pdf
http://hpctoolkit.org/training.html
Anvil: https://www.rcac.purdue.edu/software/hpctoolkit Anvil: 2021.03.01
hpcx Darwin Computational Software Hpc Tools Engineering & Technology High-Performance Computing, Scientific & Engineering Applications Support, Efficient Simulations, Data Analysis Capabilities High-Performance Computing, Scientific Computing, Data Analysis HPCx is a high-performance computing environment developed for scientific and engineering applications. It provides a platform for researchers to perform complex simulations and data analysis tasks efficiently.
hpl Expanse, Faster Benchmarking Tool Computational Software Engineering & Technology Performance Evaluation & Benchmarking Infrastructure & Instrumentation Measures The Floating-Point Rate Of Execution For Solving Linear Equations, Provides A Standardized Benchmark For Comparing Hpc Systems, Used To Assess & Rank The Performance Of Supercomputers Hpc, Benchmarking, Performance Analysis Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Expanse: Bok66Cm, De4T44F-Omp, Iyq74Za, ...
Faster: 2.3
The High Performance Linpack (HPL) benchmark is a tool for analyzing and ranking the performance of computer systems, particularly supercomputers. It measures the floating-point rate of execution for solving a dense system of linear equations. HPL is widely used to assess and compare the computational performance of High Performance Computing (HPC) systems.
hprc_utils Aces Tool Utility Engineering & Technology HPRC_utils is a collection of useful utilities to accompany software modules on the TAMU HPRC clusters. Some of the core features of hprc_utils include job submission, monitoring, resource management, data transfer, job scheduling, workflow optimization, and HPC environment setup. Hpc, High Performance Computing, Utility Tools Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.0 hprc_utils is a collection of utility tools for managing and analyzing High Performance Computing (HPC) environments and workflows.
htop Delta, Faster, Ookami Monitoring Tool System Tool Engineering & Technology This is htop, a cross-platform interactive process viewer. It is a text-mode application (for console or X terminals) and requires ncurses.
Description Source: https://htop.dev/
Real-Time Monitoring Of System Processes, Interactive Process Viewer With Easy Navigation, Color-Coded Display For Cpu, Memory, & Swap Usage, Ability To Search For Processes & Filter Based On Various Criteria, Customizable Display Options & Settings, Support For Mouse Interaction System Monitoring, Process Viewer, Resource Usage https://htop.dev/ https://linux.die.net/man/1/htop https://www.tecmint.com/htop-linux-process-monitoring/
https://www.geeksforgeeks.org/using-htop-to-monitor-system-processes-on-linux/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Delta: 3.2.2
Faster: 2.0.0, 2.0.1, 3.0.5
Ookami: 3.2.1
htop is an interactive system-monitor process-viewer for Unix systems. It provides a detailed overview of system performance and resource usage in a visually appealing and user-friendly interface.
htseq Aces, Anvil, Faster Bioinformatics Tool Python Library Biological Sciences Transcriptomics Bioinformatics HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. Quantification Of Gene Expression Levels, Handling High-Throughput Sequencing Data, RNA-Seq Data Analysis, Python Library For Bioinformatics Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/htseq
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.0.2
Anvil: 0.11.2, 0.13.5, 1.99.2, 2.0.1, 2.0.2-Py310, 2.0.2
Faster: 2.0.2
HTSeq is a Python library that provides efficient tools to work with high-throughput sequencing data. It offers functionalities to process and analyze sequence data from RNA-Seq experiments, particularly for quantification of gene and transcript expression levels.
htslib Aces, Anvil, Bridges-2, Expanse, Faster Data Processing Library Biological Sciences Next-Generation Sequencing Genomics HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by samtools and bcftools. HTSlib only depends on zlib. It is known to be compatible with gcc, g++ and clang.
Description Source: https://github.com/samtools/htslib
Support For Sam, Bam, & Cram Formats, Efficient Reading & Writing Of Sequencing Data Files, File Format Conversion & Manipulation, Indexing & Retrieval Of Sequences, Integration With Other Bioinformatics Tools Bioinformatics, Sequencing Data, File Format Processing, C Library https://www.htslib.org/ https://www.htslib.org/doc/ https://github.com/samtools/htslib/blob/develop/htslib/hts.h
https://www.htslib.org/howtos/headers.html
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/htslib
Bridges-2: https://www.psc.edu/resources/software/htslib
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.15.1
Anvil: 1.14, 1.15, 1.16, 1.17
Bridges-2: 1.13
Expanse: 4Yylg6I
Faster: 1.10.2, 1.12, 1.14, 1.15.1, 1.17
HTSlib is a C library for processing high-throughput sequencing data in the form of SAM, BAM, and CRAM formats. It allows for efficient reading, writing, and manipulation of such files, as well as various operations such as format conversion, indexing, and retrieval of specific sequences.
htstream Anvil Data Processing Tool Computational Tool Natural Sciences Genetics Biological Sciences Htstream is a quality control and processing pipeline for High Throughput Sequencing data. Key features of htstream include fast and parallel processing of short-read sequencing data, quality control and filtering of reads, mapping reads to reference genomes, generating alignment statistics, and facilitating downstream analysis such as variant calling and differential expression analysis. Bioinformatics, Sequencing Data, Data Processing Anvil: https://www.rcac.purdue.edu/software/htstream Anvil: 1.3.3 htstream is a software package that provides scalable, high-throughput tools for processing short-read sequencing data. It is designed to efficiently handle large-scale genomic datasets and perform various data processing tasks for bioinformatics applications.
https Faster Faster: https://hprc.tamu.edu/software/faster/
humann Aces, Anvil Analysis Tool Bioinformatics Biological Sciences Ecology Biological Sciences Humann is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). 1. Pathway abundance profiling from metagenomic sequencing data
2. Integration of sequence alignment and gene activity profiling
3. Quantification of microbial pathways in a community
4. Visualization tools for pathway analyses
Metagenomics, Microbiome, Pathway Analysis, Bioinformatics Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/humann
Aces: 3.6
Anvil: 3.0.0, 3.6
HUMAnN (HMP Unified Metabolic Analysis Network) is a tool for efficiently and accurately profiling the presence and abundance of microbial pathways in a community from metagenomic shotgun sequencing data. It combines sequence alignment and gene activity profiling to quantify the presence of pathway modules.
hunspell Aces, Faster Utility Spell Checking & Morphological Analysis Software Other Computer & Information Sciences Hunspell is a spell checker and morphological analyzer library and program designed for languageswith rich morphology and complex word compounding or character encoding. 1. Spell checking and suggestion capabilities. 2. Morphological analysis for complex languages. 3. Support for hyphenation, Thesaurus, and morphological generation. 4. Cross-platform compatibility. 5. Customizable and extensible dictionaries. Spell Checker, Morphological Analyzer, Language Support Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.7.1
Faster: 1.7.1
Hunspell is a spell checker and morphological analyzer software designed for languages with rich morphology and complex word compounding.
hwloc Aces, Anvil, Darwin, Delta, Expanse, Faster, Kyric, Ookami Library Library Computer & Information Sciences System Software Computer Science The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes (DRAM, HBM, non-volatile memory, CXL, etc.), sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs.
Description Source: https://www.open-mpi.org/projects/hwloc/
Some core features of hwloc include the ability to identify the hierarchy of processing units, caches, memory, and locality information, support for a variety of hardware and software platforms, APIs for querying and modifying the topology, support for NUMA (Non-Uniform Memory Access) and processor binding policies, and visualization tools. Machine Topology, Hardware Architecture, System Software https://www.open-mpi.org/projects/hwloc/ https://www.open-mpi.org/projects/hwloc/doc/v2.10.0/ https://www.open-mpi.org/projects/hwloc/tutorials/ Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/hwloc
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 2.2.0, 2.4.1, 2.5.0, 2.7.1, 2.8.0, 2.9.1, 2.9.2
Anvil: 1.11.13
Delta: 2.2.0
Expanse: 1.11.11, 2.2.0
Faster: 1.11.10, 1.11.12, 2.2.0, 2.4.1, 2.5.0, 2.7.1, 2.8.0, 2.9.1, 2.9.2
Kyric: 2.1.0
Ookami: 2.8.0
hwloc, the Portable Hardware Locality (hwloc), is an open-source hierarchical machine topology library used to provide abstract representation of the hierarchical topology of modern architectures.
hyper-shell Anvil Command-Line Tool Productivity Tool Computer & Information Sciences Process shell commands over a distributed, asynchronous queue. Some core features of hyper-shell include customizable themes and plugins, multiple panes and tabs support, advanced text editing capabilities, built-in search functionality, and extensive keyboard shortcuts. Terminal Emulator, Productivity Tool, Command-Line Interface Anvil: https://www.rcac.purdue.edu/software/hyper-shell Anvil: 2.0.2 hyper-shell is a command-line terminal replacement that aims to enhance the user experience and productivity through various features and customizations.
hyperopt Aces Python Library Computer & Information Sciences Hyperopt's job is to find the best value of a scalar-valued, possibly-stochastic function over a set of possible arguments to that function.
Description Source: https://hyperopt.github.io/hyperopt/getting-started/overview/
1. Distributed optimization: Hyperopt can distribute the optimization process across multiple compute nodes.
2. Parallel execution: Allows for parallel evaluation of the objective function.
3. Plug and play: Easily integrates with different Python libraries and frameworks, such as scikit-learn.
4. Support for various algorithms: Supports different optimization algorithms like TPE (Tree-structured Parzen Estimator) and random search.
5. Scalability: Can handle optimization problems with a large number of parameters efficiently.
Optimization, Machine Learning, Statistics https://github.com/hyperopt/hyperopt https://hyperopt.github.io/hyperopt/ https://hyperopt.github.io/hyperopt/tutorials/01.BasicTutorial/
https://github.com/hyperopt/hyperopt/wiki/FMin
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.2.7 Hyperopt is a Python library for optimizing over arbitrary search spaces. The main goal of Hyperopt is to provide a flexible and expressive architecture for an optimization workforce, including hyperparameter optimization, machine learning and statistics.
hyphen Faster Utility Tool Text Formatting/Processing Other Mathematics Generate Word Hyphenation Points, Utilizes Tex Patterns, Improves Text Justification Word Hyphenation, Text Formatting, Tex Patterns Faster: https://hprc.tamu.edu/software/faster/ Faster: 20230104 Hyphen is a command-line tool for generating word hyphenation points using the TeX patterns. It can be used to improve the appearance of justified text by splitting words at appropriate points.
hyphy Anvil Open-Source Software Analysis Tool Biological Sciences Evolutionary Biology Bioinformatics Hyphy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. Phylogenetic Analysis, Selection Analysis, Recombination Analysis, Epidemiological Modeling, Population Genetics Analysis Bioinformatics, Molecular Evolution, Phylogenetics, Epidemiology Anvil: https://www.rcac.purdue.edu/software/hyphy Anvil: 2.5.36 HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and epidemiology. It provides a flexible and user-friendly platform for conducting evolutionary analysis on biological sequence data.
hypo Anvil Scientific Software Statistical Analysis Statistics & Probability HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. 1. Conducts hypothesis testing with a variety of statistical tests
2. Calculates p-values and confidence intervals
3. Supports both parametric and non-parametric tests
4. Provides tools for power analysis and sample size calculation
5. Offers data visualization capabilities for result interpretation
Statistical Analysis, Hypothesis Testing, Data Analysis Anvil: https://www.rcac.purdue.edu/software/hypo Anvil: 1.0.3 Hypo is a software package designed for statistical analysis and hypothesis testing. It provides a range of tools for conducting various types of statistical tests and analyzing data to determine the significance of results.
hypothesis Aces, Faster Property-Based Testing Tool Testing Tool Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Hypothesis is a family of testing libraries which let you write tests parametrized by a source of examples. A Hypothesis implementation then generates simple and comprehensible examples that make your tests fail.
Description Source: https://github.com/HypothesisWorks/hypothesis
1. Automatically generates test cases based on specified properties.
2. Provides comprehensive coverage by exploring a wide range of input values.
3. Identifies edge cases and corner scenarios that traditional testing might miss.
4. Integrates with popular testing frameworks like pytest.
5. Supports custom strategies for generating complex data structures.
Python Testing Tool, Property-Based Testing, Automated Test Generation https://github.com/HypothesisWorks/hypothesis https://hypothesis.readthedocs.io/en/latest/ https://hypothesis.works/articles/getting-started-with-hypothesis/
https://hypothesis.works/articles/incremental-property-based-testing/
https://hypothesis.readthedocs.io/en/latest/quickstart.html#where-to-start
https://hypothesis.readthedocs.io/en/latest/examples.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.41.2, 6.13.1, 6.14.6, 6.46.7, 6.68.2, 6.82.0, 6.88.1, 6.90.0
Faster: 5.41.2, 5.41.5, 6.13.1, 6.14.6, 6.46.7, 6.68.2, 6.82.0
Hypothesis is a property-based testing tool for Python that helps in finding edge cases and identifying bugs by generating test data based on properties and invariants.
hypre Aces, Expanse, Faster, Stampede3 Computational Software Library Mathematics Numerical Computations Applied Mathematics HYPRE is a library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
Description Source: https://github.com/hypre-space/hypre
1. Scalable algorithms for solving large-scale linear systems. 2. Preconditioners and solvers optimized for massively parallel computers. 3. Support for various parallel computing architectures. 4. Integration with other computational software and libraries. Preconditioners, Solvers, Linear Systems, Sparse Matrices https://github.com/hypre-space/hypre https://hypre.readthedocs.io/en/latest/ https://hypre.readthedocs.io/en/latest/ch-intro.html#getting-more-information
https://github.com/hypre-space/hypre/tree/master/src/examples
https://github.com/hypre-space/hypre/wiki/Coding-Style
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2.25.0, 2.27.0, 2.31.0
Expanse: Hj2Esdx, Jj2Ap7J, ...
Faster: 2.18.2, 2.20.0, 2.21.0, 2.24.0, 2.25.0, 2.31.0
Stampede-3: 2.30.0-I64, 2.30.0
HYPRE (High Performance Preconditioners) is a library of high performance preconditioners and solvers for the solution of large, sparse linear systems of equations on massively parallel computers. It provides scalable algorithms for solving large-scale scientific and engineering applications.
iccifort Faster Programming Tool Compiler Engineering & Technology Features include advanced optimization capabilities, support for the latest C++ and Fortran language standards, debugging and profiling tools, parallel computing support, vectorization, and compatibility with various operating systems. Compiler, High-Performance Computing, Optimization Faster: https://hprc.tamu.edu/software/faster/ Faster: 2019.4.243, 2019.5.281, 2020.0.166, 2020.1.217, 2020.4.304 iccifort is a software tool that provides the Intel C++ and Fortran compilers for high-performance computing applications. These compilers are designed to optimize code performance for Intel processors.
iccifortcuda Faster Development Tools Compiler Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Hpc Compiler For Cuda-Enabled Gpus, Support For Parallel Programming, Optimized For Performance Tuning, Integration With Nvidia Cuda Architecture Hpc, Compiler, Cuda, Parallel Programming Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020B ICCIFortCUDA is a high-performance computing (HPC) compiler designed for CUDA-enabled GPUs. It provides a set of tools for developers to write and compile parallel programs using NVIDIA’s CUDA architecture.
icu Aces, Faster Libraries Utility Computer & Information Sciences Software Engineering, Systems, & Development ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. 1. Comprehensive Unicode support for wide character and locale data.
2. String handling, collation, parsing, formatting, and transliteration capabilities.
3. Time zone and calendar functionality.
4. Text layout and bi-directional text support.
5. Language-specific support for various functionalities.
6. ICU data includes support for over 300 languages.
Unicode Support, Globalization, Localization, Internationalization, Unicode Libraries https://icu.unicode.org/ https://unicode-org.github.io/icu/ https://unicode-org.github.io/icu/userguide/icu/howtouseicu.html
https://icu4c-demos.unicode.org/icu-bin/icudemos
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 67.1, 69.1, 71.1, 72.1, 73.2
Faster: 64.2, 66.1, 67.1, 69.1, 71.1, 72.1, 73.2
ICU (International Components for Unicode) is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is utilized in a vast array of applications, operating systems, and devices to provide multilingual support.
icu4c Darwin, Kyric Development Library Computer & Information Sciences Unicode Support, Globalization Support, Cross-Platform Compatibility, C/C++ & Java Libraries Unicode, Globalization, Cross-Platform, Libraries https://icu.unicode.org/ https://unicode-org.github.io/icu/ https://unicode-org.github.io/icu/userguide/icu/howtouseicu.html
https://icu4c-demos.unicode.org/icu-bin/icudemos
ICU (International Components for Unicode) is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. ICU is widely portable and gives applications the same results on all platforms and between C/C++ and Java software.
idba Anvil Assembler Ngs Assembly Biological Sciences Genomics Bioinformatics Idba is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. 1. De novo assembly of short sequencing reads.
2. Utilizes an iterative approach for optimizing assembly.
3. Designed for Illumina and 454 sequencing data.
4. High accuracy and low memory usage.
5. Handles complex and repetitive genomic regions effectively.
De Novo Assembly, Sequencing Data, Illumina, 454, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/idba Anvil: 1.1.3 IDBA (Iterative De Bruijn Graph Assembler) is a highly efficient and accurate de novo assembler for sequencing data, specifically designed for Illumina and/or 454 reads. It uses a novel iterative method to optimize the assembly of short reads into longer contigs, maintaining high accuracy and low memory consumption.
idev Stampede3 Tool Compiler Computer & Information Sciences Applied Computer Science Computer Science The idev utility creates an interactive development environment from the user's login window. In the idev window the user is connected directly to a compute node from which the user can launch MPI-compiled executables directly (with the ibrun command).
Description Source: https://tacc.utexas.edu/research/tacc-research/idev/
idev facilitates the compilation and execution of DPC++ code for GPU offloading, allowing developers to harness the power of GPUs for compute-intensive tasks. Compiler Wrapper, Dpc++ Compiler, Gpu Offloading https://tacc.utexas.edu/research/tacc-research/idev/ https://docs.tacc.utexas.edu/software/idev/ https://docs.tacc.utexas.edu/software/idev/#examples Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Stampede-3: 2.0 idev is a compiler wrapper that simplifies the use of Intel's data parallel C++ (DPC++) compiler for offloading computations to GPUs.
idl Darwin, Expanse, Stampede3 Programming Language Data Analysis & Visualization Physical Sciences IDL (Interactive Data Language) software is the trusted scientific programming language used across disciplines to create meaningful visualizations out of complex numerical data. From small-scale analysis programs to widely deployed applications, IDL provides the comprehensive computing environment you need to effectively get information from your data.
Description Source: https://www.nv5geospatialsoftware.com/Products/IDL
IDL offers a wide range of mathematical functions, statistical analysis tools, image processing capabilities, and interactive graphics for data visualization. It supports data input/output operations, array handling, and extensive libraries for various scientific and engineering applications. Software, Data Analysis, Data Visualization, Scientific Research https://www.nv5geospatialsoftware.com/Products/IDL https://www.nv5geospatialsoftware.com/docs/using_idl_home.html https://www.nv5geospatialsoftware.com/docs/Command_Line_Options_for.html
https://www.nv5geospatialsoftware.com/Learn/Videos/Video-Detail/PID/10263/mcat/18999/acat/2/evl/0/nsw/a/EDNSearch/idl
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Expanse: 8.4
Stampede-3: 8.4
IDL (Interactive Data Language) is a programming language used for data analysis, visualization, and application development. It provides a comprehensive set of tools for scientific research and data processing.
igenomes Anvil Reference Genome & Annotation Repository Bioinformatics Tool Biological Sciences Pre-Built Reference Genomes, Annotation Files, Compatibility With Popular Bioinformatics Tools, Streamlined Data Analysis Process, Regularly Updated & Curated Bioinformatics, Genomics, Reference Genomes, Annotation, Data Analysis Anvil: https://www.rcac.purdue.edu/software/igenomes Anvil: 2023-04-26 iGenomes is a collection of reference genomes and annotation files that have been pre-built for commonly used organisms, designed to streamline the data analysis pipeline for genomics research.
igprof Aces Tool Performance Profiling Engineering & Technology IgProf is a simple nice tool for measuring and analysing application memory and performance characteristics. Lightweight & Portable Performance Profiler, Supports C, C++, & Fortran Applications, Low-Overhead Measurements For Accurate Profiling, Identifies Code Hotspots For Optimization, Offers Detailed Insights Into Application Performance Profiler, Performance Analysis, Code Optimization, Software Development Aces: https://hprc.tamu.edu/software/aces/ Aces: 5.9.18
Faster: 5.9.18
igprof is a lightweight, portable, and flexible performance profiling tool for C, C++, and Fortran applications. It provides insights into code performance and helps identify hotspots for optimization, with a focus on low-overhead and accurate measurements.
igv Anvil, Faster Genomics Software Visualization Tool Biological Sciences The Integrative Genomics Viewer (IGV) is a high-performance, easy-to-use, interactive tool for the visual exploration of genomic data. It supports flexible integration of all the common types of genomic data and metadata, investigator-generated or publicly available, loaded from local or cloud sources.
Description Source: https://igv.org/doc/desktop/
IGV allows users to visualize and analyze genomic data through an interactive and user-friendly interface. Users can view aligned reads, gene expression data, variant calls, copy number variations, and more. It supports various file formats such as BAM, VCF, BED, and GFF. Users can also customize the display settings, zoom in on specific regions, and compare multiple samples side by side. Visualization, Genomics, Sequencing, Data Analysis https://igv.org/ https://igv.org/doc/desktop/#UserGuide/advanced/command_line/ https://www.youtube.com/channel/UCb5W5WqauDOwubZHb-IA_rA
https://igv.org/doc/desktop/#QuickStart/#2-load-a-reference-genome
Anvil: https://www.rcac.purdue.edu/software/igv
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 2.11.9, 2.12.3
Faster: 2.9.4-Java-11
Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, diverse genomics data sets. It supports a wide variety of data types, including next-generation sequencing data, microarrays, and genomic annotations.
iimkl Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 2022B
iimpi Aces, Faster Analytical Tool Data Analysis Biological Sciences Proteomics Bioinformatics iimpi is EasyBuild support for intel compiler toolchain (includes Intel compilers (icc, ifort), Intel MPI).
Description Source: https://docs.easybuild.io/api/easybuild/toolchains/iimpi/
1. Accurate peak integration in ion mobility-mass spectrometry data. 2. Specialized functionality for handling isobaric co-elution. 3. User-friendly interface for efficient data analysis. Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis https://docs.easybuild.io/api/easybuild/toolchains/iimpi/ https://docs.easybuild.io/api/easybuild/toolchains/iimpi/ Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021B, 2022A, 2022B, 2022.12, 2023A, 2023B, 2023.03, 2023.07
Faster: 2019B, 2020A, 2020B, 2020.12, 2021A, 2021B, 2022A, 2022B, 2022.00, 2022.05, 2022.09, ...
IIMPI (Isobaric Ion Mobility Mass Spectrometry with Peak Integration) is a software tool specifically designed for analyzing ion mobility-mass spectrometry data with a focus on accurate peak integration in the presence of isobaric co-elution.
iimpic Faster Simulation Software Computational Software Physical Sciences Condensed Matter Physics Physical Sciences 1. Implementation of the lattice Boltzmann method for porous media simulations. 2. Multi-scale modeling capabilities. 3. User-friendly Python interface for easy implementation and customization. 4. Support for various boundary conditions and fluid-solid interactions. Python Library, Porous Materials, Lattice Boltzmann Method Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020B iimpic is a Python library for multi-scale modeling of porous materials using the lattice Boltzmann method (LBM). It provides a versatile platform for simulating flow and transport phenomena in complex porous media.
imageio Aces, Faster Python Library Library Computer & Information Sciences Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 3.5+, and is easy to install.
Description Source: https://imageio.readthedocs.io/en/stable/
1. Read and write images in various formats such as JPEG, PNG, BMP, GIF, and more.
2. Support for reading and writing videos in formats like MPEG, AVI, and QuickTime.
3. Integration with NumPy arrays for efficient image processing.
4. Easily display, save, and manipulate images in Python applications.
5. Simple and uniform API for accessing image data across multiple formats.
Python Libraries, Image Processing, Data Visualization https://github.com/imageio/imageio https://imageio.readthedocs.io/en/stable/ https://imageio.readthedocs.io/en/stable/examples.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.22.2
Faster: 2.9.0, 2.13.5, 2.22.2
Imageio is a Python library that provides an easy interface to read and write a wide range of image and video file formats. It allows for simple, high-level access to image data from Python code.
imagej Aces, Faster ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine.
Description Source: https://imagej.net/ij/docs/intro.html
Image Processing, Image Analysis, Visualization Tools, Macro Recording & Scripting, Plugin Support For Extensibility Image Processing, Scientific Tool, Java-Based, Open-Source https://imagej.net/ https://imagej.net/ij/docs/guide/ https://imagej.net/tutorials/
https://imagej.net/imaging/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.53T-Java-11
Faster: 1.54B-Java-1.8
ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health. It is widely used for scientific image analysis and visualization.
imagemagick Aces, Delta, Expanse, Faster, Ookami Utility Image Processing Computer & Information Sciences ImageMagick is a free, open-source software suite, used for editing and manipulating digital images. It can be used to create, edit, compose, or convert bitmap images, and supports a wide range of file formats, including JPEG, PNG, GIF, TIFF, and PDF. Supports A Wide Range Of Image Formats, Batch Processing, Image Editing & Manipulation, Conversion Between Different Image Formats, Command-Line Interface Image Processing, Graphics Editing, Conversion Tool https://imagemagick.org/index.php https://imagemagick.org/script/command-line-tools.php https://imagemagick.org/Usage/ Aces: https://hprc.tamu.edu/software/aces/
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 7.0.11-14, 7.1.0-4, 7.1.0-37, 7.1.0-53, 7.1.1-15
Delta: 6.9, 7.1.0
Expanse: E46Spvd, ...
Faster: 7.0.10-1, 7.0.10-35, 7.0.11-14, 7.1.0-4, 7.1.0-37, 7.1.0-53
Ookami: 7.1.0
ImageMagick is a free and open-source software suite for creating, editing, composing, or converting bitmap images.
imake Aces Automation Tool Build Tools Engineering & Technology Software Engineering, Systems, & Development imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. 1. Automates the generation of makefiles for software projects
2. Allows developers to define rules for compiling source code and linking executable
3. Simplifies the build configuration process
4. Supports customization for specific project requirements
5. Integrates with the make utility for building software projects
Build Automation, Software Development, Build Configuration Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.0.8 imake is a software tool that automates the construction of imakefiles, which are used with the make utility in software development projects. It simplifies the process of generating makefiles for building software projects, allowing developers to focus on writing code rather than manually creating build configurations.
imath Aces, Faster Mathematical Modeling & Analysis Software Computational Software Mathematics Imath is a basic, light-weight, and efficient C++ representation of 2D and 3D vectors, 2x2, 3x3, and 4x4 matrices, and other simple but useful mathematical objects, functions, and data types common in computer graphics applications, including the half 16-bit floating-point type.
Description Source: https://imath.readthedocs.io/en/latest/
Some core features of iMath include symbolic and numeric computation capabilities, data visualization tools, equation solving, optimization algorithms, statistical analysis functions, and support for matrix operations. Mathematics, Computational Software, Simulation, Data Analysis https://github.com/AcademySoftwareFoundation/Imath https://imath.readthedocs.io/en/latest/ https://imath.readthedocs.io/en/latest/concepts.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.1.5, 3.1.6, 3.1.7
Faster: 3.1.5, 3.1.6, 3.1.7
iMath is a comprehensive computational software for mathematical modeling, simulation, and analysis. It provides a user-friendly interface for performing various mathematical and statistical computations.
imb Kyric Tool Benchmarking Computer & Information Sciences IMB allows users to compare different in-memory databases based on various performance metrics such as transaction throughput, response times, and scalability. It provides a standardized testing environment to ensure fair comparisons between different database systems. Benchmarking, In-Memory Databases https://imbalanced-learn.org/stable/ https://imbalanced-learn.org/stable/references/index.html#api https://imbalanced-learn.org/stable/user_guide.html#user-guide
https://imbalanced-learn.org/stable/install.html#getting-started
https://imbalanced-learn.org/stable/auto_examples/index.html#general-examples
Kyric: 2019.6 IMB stands for In-Memory Database benchmark. It is a benchmarking tool specifically designed to evaluate the performance of in-memory databases.
imbalanced-learn Aces Python Library Data Analysis Computer & Information Sciences Artificial Intelligence & Intelligent Systems Imbalanced-learn (imported as imblearn) is an open source, MIT-licensed library relying on scikit-learn (imported as sklearn) and provides tools when dealing with classification with imbalanced classes.
Description Source: https://imbalanced-learn.org/stable/
Over-Sampling Techniques (Smote, Adasyn, Etc.), Under-Sampling Techniques, Combined Over-Sampling & Under-Sampling, Ensemble Techniques (Balancedrandomforestclassifier, Rusboostclassifier), Cost-Sensitive Learning, Support For Scikit-Learn Pipeline Integration Imbalanced Datasets, Machine Learning, Classification Tasks, Python Library, Over-Sampling, Under-Sampling, Ensemble Techniques https://imbalanced-learn.org/stable/ https://imbalanced-learn.org/stable/references/index.html#api https://imbalanced-learn.org/stable/user_guide.html#user-guide
https://imbalanced-learn.org/stable/install.html#getting-started
https://imbalanced-learn.org/stable/auto_examples/index.html#general-examples
Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.10.1 Imbalanced-learn is a Python library designed to tackle the problem of imbalanced datasets in machine learning. It provides a set of tools and techniques to deal with classification tasks where the distribution of classes is skewed, with one class significantly more frequent than the others.
imkl Aces, Faster Open-Source Library Computer & Information Sciences, Artificial Intelligence & Intelligent Systems The Intel® oneAPI Math Kernel Library (oneMKL) helps you achieve maximum performance with a math computing library of highly optimized, extensively parallelized routines for CPU and GPU. The library has C and Fortran interfaces for most routines on CPU, and SYCL interfaces for some routines on both CPU and GPU.
Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html#gs.4ofwv9
The core features of imkl include graph creation, visualization, querying, and analysis functionality for knowledge graphs. It provides tools for integrating heterogeneous data sources, performing entity recognition and disambiguation, and inferring relationships between entities. Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval https://www.intel.com/content/www/us/en/developer/tools/oneapi/onemkl.html https://www.intel.com/content/www/us/en/docs/onemkl/developer-reference-c/2024-1/overview.html https://github.com/oneapi-src/oneAPI-samples/tree/master/Libraries/oneMKL/matrix_mul_mkl
https://github.com/oneapi-src/oneAPI-samples/tree/master/Libraries/oneMKL/block_cholesky_decomposition
https://www.intel.com/content/www/us/en/docs/onemkl/get-started-guide/2024-1/overview.html#GUID-618F67AE-A641-4F48-80E6-AD6D9E70FA2F
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021.4.0, 2022.1.0, 2022.2.1, 2023.0.0, 2023.1.0, 2023.2.0, 2024.0.0
Faster: 2019.5.281, 2020.1.217, 2020.4.304, 2021.1.1, 2021.2.0, 2021.3.0, 2021.4.0, 2022.0.1, 2022.1.0, 2022.2.0, ...
imkl is a open-source software library for creating and managing knowledge graphs for various applications in artificial intelligence, data science, and information retrieval.
imkl-fftw Aces, Faster Mathematical Computation Library Mathematics FFTW is a free collection of C routines for computing the discrete Fourier Transform (DFT) in one or more dimensions, and provides portability across platforms. The Intel Math Kernel Library (MKL) offers FFTW2 (for version 2.x) and FFTW3 (for version 3.x) interfaces to the Intel MKL Fast Fourier Transform and Trigonometric Transform functionality. These interfaces enable applications using FFTW to gain performance with Intel MKL without changing the application source code.
Description Source: https://www.nas.nasa.gov/hecc/support/kb/mkl-fftw-interface_204.html
1. Integration of Intel Math Kernel Library (IMKL) for optimized mathematical functions.
2. Utilizes the Fastest Fourier Transform in the West (FFTW) for efficient Fourier transform computations.
3. High performance on Intel architectures for Fourier transform operations.
Software Library, Math Library, Mathematical Computation, Fourier Transforms, High-Performance Computing https://www.nas.nasa.gov/hecc/support/kb/mkl-fftw-interface_204.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021.4.0, 2022.1.0, 2022.2.1, 2023.0.0, 2023.1.0, 2023.2.0
Faster: 2021.4.0, 2022.0.1, 2022.1.0, 2022.2.0, 2022.2.1, 2023.0.0, 2023.1.0, ...
imkl-fftw is a library that combines Intel Math Kernel Library (IMKL) with FFTW (Fastest Fourier Transform in the West) for high-performance computation of Fourier transforms on Intel architectures.
iml Aces R Package Machine Learning Interpretability Computer & Information Sciences IML is a free library of C source code which implements algorithms for computing exact solutions to dense systems of linear equations over the integers. iml is an R package that enables interpretable machine learning for regression and classification models. It provides a suite of tools for understanding the predictions of machine learning models by creating interpretable explanations. Machine Learning, Interpretability, Model Explanation Aces: https://hprc.tamu.edu/software/aces/ Aces: 1.0.5 Interpretable Machine Learning
impi Aces, Anvil, Faster, Stampede3 Communication Library Library Engineering & Technology impi is an intel MPI implementation. It is included in the Intel-2017.4 compiler. It is a good compiler for MPI programming on Xeon Phi.
Description Source: https://hpc.loni.org/docs/guides/software.php?software=impi#
impi offers efficient communication among processes, supports scalable performance for large-scale parallel computing, and has advanced queuing mechanisms for managing message passing in distributed computing environments. Message Passing Library, Parallel Computing, Asynchronous Messaging https://www.intel.com/content/www/us/en/developer/tools/oneapi/mpi-library.html#gs.5295ue https://www.intel.com/content/www/us/en/docs/mpi-library/developer-reference-linux/2021-12/overview.html https://www.intel.com/content/www/us/en/docs/mpi-library/get-started-guide-linux/2021-11/overview.html Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/impi
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2021.4.0, 2021.6.0, 2021.7.1, 2021.8.0, 2021.9.0, 2021.10.0, 2021.11.0
Anvil: 2019.5.281
Faster: 2018.5.288, 2019.7.217, 2019.9.304, 2021.1.1, 2021.2.0, 2021.3.0, 2021.4.0, 2021.5.0, 2021.6.0, 2021.7.0, ...
Stampede-3: 21.9, 21.11
impi is a high-performance message passing library that provides asynchronous messaging and queuing functionalities for parallel computing applications.
impute2 Anvil Tool Bioinformatics Biological Sciences Genome-Wide Association Studies Genetics Impute2 is a genotype imputation and haplotype phasing program. IMPUTE2 uses a combination of reference haplotypes and the study genotypes to infer genotypes at ungenotyped SNPs. It also provides a quality score to assess the imputation accuracy. The software supports a variety of input formats and allows for parallel computing to speed up the imputation process. Genotype Imputation, Genome-Wide Association Studies, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/impute2 Anvil: 2.3.2 IMPUTE2 is a tool for imputing ungenotyped markers in large-scale genome-wide association studies.
infernal Anvil, Bridges-2 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
Description Source: http://eddylab.org/infernal/
1. Searching DNA sequence databases for RNA structure and sequence similarities
2. Aligning RNA sequences to RNA sequence and structural models
3. Building covariance models
4. Detecting RNA homologs
RNA Sequence Analysis, Bioinformatics, Sequence Alignment http://eddylab.org/infernal/ http://eddylab.org/infernal/Userguide.pdf https://github.com/EddyRivasLab/infernal/blob/master/documentation/userguide/tutorial.tex Anvil: https://www.rcac.purdue.edu/software/infernal
Bridges-2: https://www.psc.edu/resources/software/infernal
Anvil: 1.1.4
Bridges-2: 1.1.3
Infernal is a software for searching DNA sequence databases for RNA structure and sequence similarities. It is used to align RNA sequences to RNA sequence and structural models.
init_opencl Kyric Software Development Library Computer & Information Sciences Initialize Opencl Platforms, Create Opencl Contexts, Support For Parallel Computing Applications Software, Compiler, Library, Hpc Kyric: Latest, 2021.1.1 init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications.
inputproto Delta Library Development Tools Computer & Information Sciences Provides the necessary headers for compiling Xlib clients. Software Development, Headers, Xlib Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2.3.2 A package that provides the headers used to compile Xlib clients.
inq Faster Command-Line Interface Tools Computer & Information Sciences, Other Computer & Information Sciences Create & Manage Inventory Data In Yaml Format, Query Inventory Data Using A Simple Command-Line Interface, Use Filters & Search Queries To Extract Specific Information, Facilitates System Administration Tasks Related To Inventory Management Inventory Management, System Administration Faster: https://hprc.tamu.edu/software/faster/ Faster: 20230821 inq is a command-line tool for managing and querying inventory data in YAML format. It allows users to easily manipulate and search inventory data for system administration tasks.
inspector Kyric Security Software Monitoring Tool Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Key features include real-time monitoring of network traffic, system performance metrics, and security events. It provides alerts for suspicious activities, generates reports for analysis, and allows for proactive response to potential threats. Monitoring, Security, Network Analysis https://www.intel.com/content/www/us/en/developer/tools/oneapi/inspector.html#gs.52c03e https://www.intel.com/content/www/us/en/docs/inspector/user-guide-linux/2024-1/overview.html https://www.intel.com/content/www/us/en/docs/inspector/get-started-guide/2024-1/linux.html
https://www.intel.com/content/www/us/en/developer/articles/training/inspector-tutorials.html
Kyric: Latest, 2021.1.1 Inspector is a software tool used for monitoring and analyzing various aspects of computer systems and networks to detect and prevent security breaches or performance issues.
instrain Anvil Python Library Library Biological Sciences Metagenomics, Microbial Ecology Bioinformatics Instrain is a python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification. 1. Strain-level composition identification in metagenomic data
2. Variant identification specific to different strains within a microbial community
3. Analysis of strain heterogeneity and evolution within microbial populations
Metagenomics, Microbial Community, Strain Identification, Variant Analysis Anvil: https://www.rcac.purdue.edu/software/instrain Anvil: 1.5.7, 1.6.3 instrain is a python package for identifying strains in metagenomic data. It allows users to infer strain-level composition of metagenomes and identify variants specific to different strains within a microbial community.
intarna Anvil Bioinformatics Tool Prediction Tool Biological Sciences Bioinformatics Biological Sciences Intarna is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. 1. Prediction of RNA-RNA interactions
2. Consideration of target site accessibility
3. Calculation of hybridization energies
4. Identification of energetically favorable interaction sites
5. Accessibility calculation in target RNA
RNA-RNA Interaction Prediction, Bioinformatics, RNA Structure Prediction Anvil: https://www.rcac.purdue.edu/software/intarna Anvil: 3.3.1 IntaRNA predicts RNA-RNA interactions by taking both target site accessibility and hybridization energies into account, allowing the identification of interaction sites that are not only energetically favorable, but also accessible in the target RNA.
intel Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Kyric, Stampede3 Hardware Enterprise Software Engineering & Technology Intel Compilers. Intel Parallel Studio XE 2020 Cluster Edition is an advanced, comprehensive C ++ and Fortran tool suite that simplifies and speeds HPC and cluster application development , debug, and tuning. Intel offers a wide range of products including processors, integrated graphics solutions, system-on-chip products, and more. Their technology powers a variety of devices and applications across different industries. Semiconductor, Technology, Microprocessors Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/intel
Bridges-2: https://www.psc.edu/resources/software/intel
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/
Aces: 2023.1.0, 2023.2.0, 2023.2.0.231103
Anvil: 19.0.5.281
Bridges-2: 20.4, 2021.3.0, 2021.10.0
Delta: 2022.2.1, 2024.0.0
Expanse: Vecir2B, 6Pv46So
Faster: Toolkits, 2019B, 2020A, 2020B, 2020.12, 2021A, 2021B, 2022A, 2022B, 2022.00, 2022.05, ...
Kyric: 19.1.3.304
Ookami: Tbb/64/2020/20.0.2
Stampede-3: 23.1, 24.0
Intel is a multinational corporation that designs and manufactures semiconductor chips and other technology products. The company is a leading provider of microprocessors for personal computers, servers, and other computing devices.
intel compiler Jetstream Development Tools Compiler Computer & Information Sciences The Intel Compiler provides advanced optimization features to enhance application performance, including auto-vectorization, parallelization, and profile-guided optimization. It supports the latest language standards and includes tools for debugging and performance analysis. Compiler, Optimization, Performance, Debugging The Intel Compiler is a suite of high-performance compilers from Intel for various programming languages, including C, C++, and Fortran. It is designed to maximize application performance on Intel architecture-based processors.
intel_ai_toolkit Delta Compilers Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2023.1
intel_ipp_ia32 Kyric Compilers Kyric: Latest, 2021.1.1
intel_ipp_intel64 Kyric Commercial Library Computer & Information Sciences, Software Engineering, Systems, & Development 1. Optimized functions for signal processing, imaging, cryptography, and data processing. 2. Support for various data formats and algorithms. 3. High performance on Intel architecture. 4. Multi-threading and SIMD support for parallel processing. 5. Integration with popular development environments and languages. Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography Kyric: Latest, 2021.1.1 Intel Integrated Performance Primitives (Intel IPP) provides high-performance software libraries that are designed to help developers improve the performance of their applications. Intel IPP offers a wide range of functions that are optimized for Intel architecture, including signal, imaging, cryptography, and data processing algorithms.
intel_ippcp_ia32 Kyric Compiler/Library Library Computer & Information Sciences Optimized Encryption & Decryption Algorithms, Support For Various Cryptographic Techniques, Designed For Intel Architecture Processors, Improved Performance In Cryptographic Operations Cryptographic Library, Performance Optimization, Intel Architecture Kyric: Latest, 2021.1.1 Intel Integrated Performance Primitives - Cryptography (IPP-Crypto) is a library that provides highly optimized building blocks for a variety of encryption and decryption algorithms on Intel architecture processors. It aims to accelerate cryptographic operations to enhance performance in software applications.
intel_ippcp_intel64 Kyric Optimization Library Library Computer & Information Sciences Optimized Cryptographic Functions For Intel Processors, High-Performance Encryption & Decryption Algorithms, Support For A Variety Of Cryptographic Operations, Integration With Intel Ipp Library For Additional Performance Optimizations Cryptography, High-Performance Computing, Intel Processors, Security Kyric: Latest, 2021.1.1 Intel Integrated Performance Primitives Cryptography (IPP Cryptography) is a collection of highly optimized cryptographic functions and algorithms developed by Intel for high-performance computing applications. It provides a set of cryptographic functions optimized for Intel processors to enhance the security and performance of cryptographic operations in software.
intel-advisor Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-advisor Bridges-2: 2023.2.0
intel-ccl Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-ccl Bridges-2: 2021.10.0
intel-compiler Bridges-2 Development Tools Compiler Computer & Information Sciences Software Engineering, Systems, & Development Computer Science 1. Advanced optimizations for Intel processors
2. Support for C, C++, and Fortran languages
3. Performance tuning capabilities
4. Vectorization and parallelization support
5. Interoperability with existing codebases
6. Integration with Intel architecture-based platforms
Compiler, Optimization, Performance, Parallelization Bridges-2: https://www.psc.edu/resources/software/intel-compiler Bridges-2: 2023.2.1 The Intel Compiler suite is a set of optimizing compilers with support for C, C++, and Fortran languages. It provides advanced optimizations and performance tuning for applications running on Intel architecture-based platforms.
intel-compiler-rt Bridges-2 Compiler Runtime Library Library Computer & Information Sciences 1. Provides runtime support for applications compiled with Intel compilers
2. Includes optimized libraries for performance-critical functions
3. Supports advanced processor optimizations
4. Enhances application performance and reliability
5. Enables better scalability and parallelism
Compiler, Runtime Library, Performance Optimization Bridges-2: https://www.psc.edu/resources/software/intel-compiler-rt Bridges-2: 2023.2.1 The Intel Compiler Runtime Library (Intel Compiler RT) is a collection of runtime libraries for the Intel software development tools, designed to provide support for various runtime components in software applications compiled with Intel compilers.
intel-compiler-rt32 Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-compiler-rt32 Bridges-2: 2023.2.1
intel-compiler32 Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-compiler32 Bridges-2: 2023.2.1
intel-compilers Aces, Faster Compilers Intel C, C++ & Fortran compilers (classic and oneAPI) Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2021.2.0, 2021.4.0, 2022.1.0, 2022.2.0, 2022.2.1, ...
Faster: 2021.1.2, 2021.2.0, 2021.3.0, 2021.4.0, 2022.0.1, ...
intel-dal Bridges-2 1. Secure environment for executing trusted applications
2. Ability to dynamically load and execute small code modules
3. Provides isolation and protection mechanisms
4. Streamlines the process of developing and deploying applications
5. Supports multiple platforms and languages
Security, Intel Platform, Dynamic Code Loading, Trusted Applications Bridges-2: https://www.psc.edu/resources/software/intel-dal Bridges-2: 2023.2.0 Intel Dynamic Application Loader (DAL) is a framework that enables applications to dynamically load and execute small code modules. It provides a secure environment for executing trusted applications on Intel platforms.
intel-debugger Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-debugger Bridges-2: 2023.2.0
intel-dev-utilities Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-dev-utilities Bridges-2: 2021.10.0
intel-dnnl Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-dnnl Bridges-2: 2023.2.0
intel-dnnl-cpu-gomp Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-dnnl-cpu-gomp Bridges-2: 2023.2.0
intel-dnnl-cpu-iomp Bridges-2 Tool Library Computer & Information Sciences 1. Accelerated deep learning operations on Intel CPUs.
2. Integration with deep learning frameworks like TensorFlow and PyTorch.
3. Support for various neural network layer types.
4. Enhanced performance through optimizations for Intel architecture.
5. Scalability for large-scale deep learning models.
Deep Learning, Cpu Optimization, Neural Networks Bridges-2: https://www.psc.edu/resources/software/intel-dnnl-cpu-iomp Bridges-2: 2023.2.0 The Intel oneAPI Deep Neural Network Library (DNNL) for CPU with Intel oneAPI Math Kernel Library (iomp) is a high-performance library for deep learning applications optimized for Intel CPUs. It provides highly optimized functions for deep learning frameworks and applications to accelerate training and inference tasks.
intel-dnnl-cpu-tbb Bridges-2 Deep Learning Library Library Computer & Information Sciences Machine Learning Artificial Intelligence & Intelligent Systems 1. High-performance deep learning library optimized for Intel CPUs. 2. Supports various neural network models and operations. 3. Integration with Threading Building Blocks (TBB) for efficient multi-threading. 4. Provides primitives for deep learning acceleration on Intel CPUs. Deep Learning, Neural Networks, Cpu Optimization, Threading Building Blocks Bridges-2: https://www.psc.edu/resources/software/intel-dnnl-cpu-tbb Bridges-2: 2023.2.0 Intel oneAPI Deep Neural Network Library (DNNL) for CPU with Threading Building Blocks (TBB) support is a high-performance library for deep learning applications. It provides optimized building blocks for implementing deep neural networks on Intel CPUs.
intel-dpct Bridges-2 Compiler Tool Computer & Information Sciences 1. Automatic translation of CUDA source code to DPC++ source code. 2. Support for CUDA kernels defined in separate files. 3. Generation of DPC++ offload syntax for given CUDA kernel code. 4. Integration with Intel Advisor & Inspector tools for analysis and optimization of the code. 5. Compatible with Intel oneAPI toolkits for cross-architecture development. Intel, Data Migration, Cuda, Dpc++, Heterogeneous Computing Bridges-2: https://www.psc.edu/resources/software/intel-dpct Bridges-2: 2023.2.0 Intel Data Parallel C++ (DPC++) Compatibility Tool (dpct) is a tool developed by Intel to facilitate migration of CUDA kernels to Data Parallel C++ (DPC++) for seamless porting to heterogeneous platforms.
intel-dpl Bridges-2 Development Tool Parallel Programming Library Computer & Information Sciences Easy-To-Use Parallel Programming Interface, Support For Task Parallelism & Data Parallelism, High Performance Computing Capabilities, Optimized For Intel Architectures Parallel Programming, High Performance Computing, Intel Architecture Bridges-2: https://www.psc.edu/resources/software/intel-dpl Bridges-2: 2022.2.0 Intel-DPL (Data Parallel Library) is a software library that enables developers to write parallel programs in a natural and expressive way, without needing to have expertise in parallel programming. It helps in achieving high performance in parallel computing tasks by utilizing task parallelism and data parallelism.
intel-icc Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-icc Bridges-2: 2023.2.1
intel-icc32 Bridges-2 Development Tools Compiler Computer & Information Sciences 1. Support for 32-bit architectures
2. Optimization for Intel processors
3. Building and compiling applications
4. Integration with Intel libraries
5. Parallel computing support
Compiler, Software Development, Optimization Bridges-2: https://www.psc.edu/resources/software/intel-icc32 Bridges-2: 2023.2.1 The intel-icc32 compiler is a part of the Intel Compiler Suite specifically designed for 32-bit architectures. It provides a set of tools and libraries for optimizing and building applications for Intel processors.
intel-inspector Bridges-2 Memory & Threading Error Checker Debugging Tool Engineering & Technology 1. Detects memory leaks and errors in multithreaded applications.
2. Provides highly detailed error analysis and debugging capabilities.
3. Supports serial and multithreaded applications on Windows and Linux platforms.
4. Offers comprehensive data race and deadlock detection.
Software, Development, Debugging, Memory Management, Multithreading Bridges-2: https://www.psc.edu/resources/software/intel-inspector Bridges-2: 2023.2.0 The Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and multithreaded applications on Windows or Linux operating systems. It helps developers find memory and threading errors early in the code development cycle to eliminate costly and time-consuming issues that might otherwise arise later in the development phase or in the field.
intel-ipp-ia32 Bridges-2 Shared Library Library Computer & Information Sciences Software Engineering, Systems, & Development Computer Science 1. Optimized routines for signal and data processing.
2. High-performance functions for image processing.
3. Cryptography functions for secure data handling.
4. Support for various domains and applications.
5. Platform-specific optimizations for IA-32 architecture.
Software Library, Performance Optimization, Signal Processing, Image Processing, Cryptography Bridges-2: https://www.psc.edu/resources/software/intel-ipp-ia32 Bridges-2: 2021.9.0 Intel Integrated Performance Primitives (Intel IPP) for IA-32 architecture is a software library that provides a comprehensive set of high-performance functions for building advanced applications in various domains. It offers optimized routines for signal and data processing, image processing, cryptography, and more.
intel-ipp-intel64 Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-ipp-intel64 Bridges-2: 2021.9.0
intel-ippcp-ia32 Bridges-2 Program Library Library Computer & Information Sciences 1. Optimized cryptographic functions for encryption and decryption.
2. Support for digital signatures and authentication mechanisms.
3. Accelerated performance on Intel processors.
4. Broad range of cryptographic algorithms, including AES, RSA, and SHA.
Software Library, Cryptography, Security Bridges-2: https://www.psc.edu/resources/software/intel-ippcp-ia32 Bridges-2: 2021.8.0 Intel Integrated Performance Primitives (IPP) Cryptography (IPP-Crypto) is a library of high-performance cryptographic and security functions optimized for Intel processors. It provides developers with a broad range of encryption, digital signature, and authentication functionality to secure data and communications.
intel-ippcp-intel64 Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-ippcp-intel64 Bridges-2: 2021.8.0
intel-itac Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-itac Bridges-2: 2021.10.0
intel-mkl Anvil, Bridges-2, Darwin, Expanse Compilers Intel Math Kernel Library (MKL) contains ScaLAPACK, LAPACK, Sparse Solver, BLAS, Sparse BLAS, CBLAS, GMP, FFTs, DFTs, VSL, VML, and Interval Arithmetic routines. https://www.rcac.purdue.edu/index.php/knowledge/applications/intel-mkl https://www.intel.com/content/www/us/en/resources-documentation/developer.html#gs.5q9gn8 Anvil: https://www.rcac.purdue.edu/software/intel-mkl
Bridges-2: https://www.psc.edu/resources/software/intel-mkl
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 2019.5.281, 2020.4.304
Bridges-2: 2023.2.0
Expanse: Flrwt2M, ...
intel-mkl32 Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-mkl32 Bridges-2: 2023.2.0
intel-mpi Bridges-2, Expanse Bridges-2: https://www.psc.edu/resources/software/intel-mpi
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Bridges-2: 2021.10.0
Expanse: Ezrfjne, ...
intel-oclfpga Bridges-2 Compiler Development Tools Computer & Information Sciences Software Engineering, Systems, & Development Computer Science Unified Programming Model For Cpu, Gpu, & Fpga, Optimized Performance For Intel Fpga Devices, Support For Opencl Programming Language, Integration With Intel Oneapi Base Toolkit Development Tools, Accelerating Workloads, Fpga Programming, Hardware Acceleration Bridges-2: https://www.psc.edu/resources/software/intel-oclfpga Bridges-2: 2023.2.1 The Intel OneAPI Base Toolkit for OpenCL FPGA is a comprehensive suite of development tools for accelerating workloads on Intel FPGA devices. It provides a unified programming model for CPU, GPU, and FPGA to simplify application development and deployment across diverse hardware architectures.
intel-oneapi Bridges-2, Darwin Bridges-2: https://www.psc.edu/resources/software/intel-oneapi Bridges-2: 2023.2.1
Jetstream: 2023.0.0
intel-oneapi-advisor Delta Compilers Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2024.0.0
intel-oneapi-compilers Delta Compilers Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2022.2.1, ...
intel-oneapi-mkl Darwin, Delta Compilers Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2024.0.0
intel-oneapi-mpi Delta Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 2021.11.0
intel-python Darwin, Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 2022.1.0
intel-tbb Bridges-2, Delta, Expanse Bridges-2: https://www.psc.edu/resources/software/intel-tbb
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Bridges-2: 2021.10.0
Delta: 2021.9.0
Expanse: 2020.3
intel-tbb32 Bridges-2 Library Development Tools Computer & Information Sciences, Computer Science, Applied Computer Science 1. Parallel algorithms and containers for C++.
2. Task scheduler framework for managing parallel workloads.
3. Scalability features for efficient multi-core utilization.
4. Portable and easy-to-use API for developers.
Parallelism, C++, Multi-Core, Library Bridges-2: https://www.psc.edu/resources/software/intel-tbb32 Bridges-2: 2021.10.0 Intel Threading Building Blocks (TBB) is a widely-used C++ library for parallelism. It provides a way to write parallel C++ programs that take full advantage of multi-core processors.
intel-vtune Bridges-2 Bridges-2: https://www.psc.edu/resources/software/intel-vtune Bridges-2: 2023.2.0
intelcuda Faster Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020B
intelmpi Bridges-2 Library Development Tools Engineering & Technology Intel MPI Libriaries. This module loads the Intel MPI implementation along with the Intel Compilers. High Performance Computing (Hpc), Message Passing Interface (Mpi) Library, Optimized For Intel Architecture Hpc, Mpi Library, Intel Architecture Bridges-2: https://www.psc.edu/resources/software/intelmpi Bridges-2: 20.4-Intel20.4, 2021.3.0-Intel2021.3.0, ... Intel MPI Library focuses on enabling applications to perform better on Intel architecture-based clusters. It enables applications to gain faster communication performance on Intel Xeon Phi coprocessors and Intel Xeon processors.
interproscan Anvil, Faster Bioinformatics Tool Annotation Tool Biological Sciences Proteomics Bioinformatics Interproscan is the software package that allows sequences to be scanned against InterPro's member database signatures. Protein Sequence Analysis, Functional Classification, Domain Prediction, Signature Recognition Bioinformatics, Proteomics, Sequence Analysis, Functional Annotation Anvil: https://www.rcac.purdue.edu/software/interproscan
Faster: https://hprc.tamu.edu/software/faster/
Anvil: 5.54_87.0, 5.61-93.0
Faster: 5.52-86.0
InterProScan is a software tool that allows the functional analysis of protein sequences by classifying them into families and predicting domains and important sites. It combines different protein signature recognition methods in one resource.
intltool Aces, Faster Localization Tool Tools Computer & Information Sciences intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
Description Source: https://freedesktop.org/wiki/Software/intltool/
1. Parsing and merging of existing translations. 2. Extraction of translatable strings from source code. 3. Generation of output files in different formats. Localization, Translation, Internationalization https://freedesktop.org/wiki/Software/intltool/ https://code.launchpad.net/intltool https://github.com/Distrotech/intltool/blob/master/README
https://github.com/Distrotech/intltool/blob/master/doc/I18N-HOWTO
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.51.0
Faster: 0.51.0
Intltool is a set of tools to centralize translation of many different file formats using a single language-styled file.
iomkl Faster Library Computational Software Mathematics Optimized For Modern Intel Cpus, High-Performance Mathematical Operations, Efficient Linear Algebra Computations Math Kernel Library, High-Performance Computing, Linear Algebra, Mathematical Operations Faster: https://hprc.tamu.edu/software/faster/ Faster: 2021A, 2022.00 IOMKL is a high-performance Mathematical Kernel Library (MKL) for Intel's Math Kernel Library developed for modern Intel CPUs. It is optimized for various mathematical operations and linear algebra computations.
iompi Faster Library Simulation Software Physical Sciences Computational Physics Applied Mathematics 1. Provides a comprehensive set of tools for efficiently solving linear and nonlinear PDEs.
2. Supports a variety of numerical methods, such as finite element methods (FEM), finite difference methods (FDM), and spectral methods.
3. Offers support for parallel computing and can leverage high-performance computing (HPC) resources.
4. Includes pre-built solvers for common PDEs and allows users to implement custom solvers.
5. Enables easy integration with existing simulation codes and software packages.
Computational Software, Numerical Methods, Partial Differential Equations, Scientific Computing Faster: https://hprc.tamu.edu/software/faster/ Faster: 2020B, 2021A, 2022.00 IOMPI (Integrated Operator Methods Package Interface) is a software framework designed to facilitate the development and implementation of operator-based numerical methods for solving partial differential equations (PDEs) in computational physics and engineering.
ior Delta, Expanse Utility Software Performance Analysis Tool Computer Science High-Performance Computing Computer Science I/O performance analysis, Parallel I/O optimization, Benchmarking, Profiling High-Performance Computing, Parallel Computing, I/O Optimization Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Delta: 3.3.0
Expanse: C3Prdsv, C5Wdybp, Fbtdgli, ...
ior is a versatile software tool for analyzing and optimizing input/output (I/O) performance in high-performance computing (HPC) systems. It is designed to assess and improve the efficiency of data transfer operations in parallel computing environments.
iperf3 Delta Tool Network Testing Computer & Information Sciences 1. Measures TCP, UDP, and SCTP bandwidth performance
2. Supports IPv4 and IPv6
3. Option for bidirectional testing
4. Customizable testing parameters
5. Supports client-server architecture
6. Real-time measurements and statistics
Network Testing, Bandwidth Measurement, Network Performance Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 3.6 iperf3 is a tool for actively measuring the maximum achievable bandwidth on IP networks. It supports various parameters to customize the testing process and is widely used for network performance testing and tuning.
ipmitool Ookami Utility System Management Engineering & Technology ipmitool is a utility for managing and configuring devices that support the Intelligent Platform Management Interface. IPMI is an open standard for monitoring, logging, recovery, inventory, and control of hardware that is implemented independent of the main CPU, BIOS, and OS.
Description Source: https://github.com/ipmitool/ipmitool
Retrieve System Information Remotely, Configure & Manage Ipmi-Enabled Devices, Monitor Hardware Sensors & Power Usage, Reset Or Power Cycle Systems Remotely, Execute Pre-Defined Commands On Remote Machines System Management, Hardware Monitoring, Remote Administration, Open Source https://github.com/ipmitool/ipmitool https://www.mankier.com/1/ipmitool https://www.mankier.com/1/ipmitool#Examples Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 1.8.18 ipmitool is an open-source utility for managing and configuring devices that support the Intelligent Platform Management Interface (IPMI) specification. It allows users to interact with IPMI-enabled devices to retrieve information, perform system management tasks, and monitor hardware sensors remotely.
ipython Aces, Faster Development Tools Interpreter Computer & Information Sciences Software Engineering, Systems, & Development Computer Science IPython is BSD-licensed, open-source software that is developed as a set of Subprojects under the ipython Github organization. These Subprojects are all part of the larger Project Jupyter umbrella. For further information about project governance, sponsorship and development, please see the Project page on Jupyter’s website.
Description Source: https://ipython.org/project.html
Interactive Python Shell With Enhancements, Support For Data Visualization & Data Analysis, Parallel Computing Capabilities, Rich Media Integration, Integration With Other Programming Languages Command Shell, Interactive Computing, Data Visualization, Parallel Computing, Data Analysis https://ipython.org/ https://ipython.readthedocs.io/en/stable/ https://ipython.readthedocs.io/en/stable/interactive/tutorial.html Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 7.26.0, 8.5.0, 8.14.0
Faster: 7.15.0-Python-3.8.2, 7.18.1, 7.26.0, 8.5.0
IPython is a powerful interactive command shell that provides a robust and flexible environment for interactive computing. It offers features such as easy-to-use, high-performance tools for parallel computing, data visualization, and data analysis.
iq-tree Expanse Phylogenetic Tree Construction Tool Bioinformatics Software Biological Sciences Phylogenetics Systematics & Population Biology Phylogenomic Inference, Substitution Models, Ultrafast Bootstrap Approximation, Maximum Likelihood Estimation Phylogenetics, Bioinformatics, Computational Biology, Phylogenomic Analysis Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Lvmeedg-Omp IQ-TREE is a fast and effective software for phylogenomic inference. It implements a variety of models for DNA and protein sequences, including substitution models, rate heterogeneity, and mixture models. IQ-TREE uses maximum likelihood estimation to construct phylogenetic trees, and offers ultrafast bootstrap approximation to assess the tree accuracy.
iqtree Anvil IQ-TREE is an efficient phylogenomic software by maximum likelihood. Anvil: https://www.rcac.purdue.edu/software/iqtree Anvil: 1.6.12, 2.1.2, 2.2.0_Beta, 2.2.2.2
iqtree2 Anvil IQ-TREE is an efficient phylogenomic software by maximum likelihood. Anvil: https://www.rcac.purdue.edu/software/iqtree2 Anvil: 2.2.2.6, 2.2.2.9
irods-icommands Bridges-2 iCommands, the default command line interface to iRODS. Bridges-2: https://www.psc.edu/resources/software/irods-icommands Bridges-2: 4.3.0
isa-l Aces, Faster Engineering & Technology The Intel® Intelligent Storage Acceleration Library (Intel® ISA-L) provides tools to minimize disk space use and maximize storage throughput, security, and resilience. Learn about its optimized functions for RAID, erasure code, cyclic redundancy check (CRC) functions, cryptographic hash, encryption, and compression.
Description Source: https://www.intel.com/content/www/us/en/developer/tools/isa-l/overview.html
Optimized Low-Level Functions, High-Performance Data Movement, Data Protection Functions, Leverages Intel Hardware Capabilities Optimized Functions, Data Movement, Data Protection, Storage Applications https://www.intel.com/content/www/us/en/developer/tools/isa-l/overview.html https://github.com/intel/isa-l/blob/master/doc/functions.md https://www.intel.com/content/www/us/en/developer/videos/intelligent-storage-acceleration-library.html
https://github.com/intel/isa-l/tree/master/examples
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.30.0
Faster: 2.30.0
ISA-L (Intel Storage Acceleration Library) is a collection of optimized low-level functions used in storage applications. It is specifically designed to offer high-performance data movement and protection functions for storage and data processing workloads, leveraging Intel hardware capabilities.
isl Aces, Faster Library Computational Software Computer & Information Sciences Applied Computer Science Computer Science isl is a library for manipulating sets and relations of integer points bounded by linear constraints. - Manipulating sets and maps of integer points
- Computing integer points in a set
- Intersection and union operations
- Projection of a set
- Affine transformations
Library, Integer Points, Linear Constraints Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.26
Faster: 0.26
ISL (Integer Set Library) is a library for manipulating sets and maps of integer points bounded by linear constraints. It provides functions for computing the integer points in a set or projection of a set represented as unions of polyhedra, as wells as their images under affine transformations.
ismapper Anvil Analysis Tool Bioinformatics Tools Biological Sciences ISMapper searches for IS positions in sequence data using paired end Illumina short reads, an IS query/queries of interest and a reference genome. ISMapper reports the IS positions it has found in each isolate, relative to the provided reference genome. Accurate Mapping & Quantification Of Isomirs, Identification Of Differentially Expressed Isomirs, Analysis Of Small RNA-Seq Data, Visualization Of Isomir Expression Patterns Bioinformatics, Computational Biology, Small RNA-Seq, Mirna Analysis Anvil: https://www.rcac.purdue.edu/software/ismapper Anvil: 2.0.2 Ismapper is a software for isomiR identification and differential expression analysis from small RNA-seq data. It is designed to accurately map and quantify isomiRs, which are isoforms of microRNAs resulting from alternative precursor processing and post-transcriptional modifications.
isoquant Anvil Productivity Software Economic Modeling Tool Social Sciences Production Analysis Economics IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. 1. Production analysis: Helps in determining the most efficient input combinations for a given level of output. 2. Isoquant mapping: Visualizes the various combinations of inputs that yield the same level of output. 3. Cost minimization: Assists in minimizing production costs while maximizing output. 4. Input substitution: Evaluates the impact of substituting one input for another on production efficiency. Production Analysis, Input-Output Relationships, Economics Anvil: https://www.rcac.purdue.edu/software/isoquant Anvil: 3.1.2 Isoquant is a software tool used in economics to analyze production processes and determine the optimal combination of inputs to produce a given level of output. It is commonly used to study the trade-offs between factors of production such as labor and capital in maximizing output.
isoseq3 Anvil Anvil: https://www.rcac.purdue.edu/software/isoseq3 Anvil: 3.4.0, 3.7.0, 3.8.2
itac Kyric, Stampede3 Compiler Performance Analysis Tool Computer & Information Sciences The Intel® Trace Analyzer and Collector profiles and analyzes MPI applications to help focus your optimization efforts.
Description Source: https://www.intel.com/content/www/us/en/developer/tools/oneapi/trace-analyzer.html#gs.4oj2fp
ITAC offers features such as tracing and profiling of parallel applications, identifying performance bottlenecks, visualizing application performance data, analyzing communication patterns, and providing detailed reports on the performance metrics. Performance Analysis, Parallel Applications, Optimization https://www.intel.com/content/www/us/en/developer/tools/oneapi/trace-analyzer.html https://www.intel.com/content/www/us/en/docs/trace-analyzer-collector/user-guide-reference/2021-10/overview.html https://www.intel.com/content/www/us/en/docs/trace-analyzer-collector/get-started-guide/2021-10/overview.html
https://www.intel.com/content/www/us/en/docs/vtune-profiler/tutorial-vtune-itac-mpi-openmp/2020/overview.html
https://www.intel.com/content/www/us/en/docs/trace-analyzer-collector/tutorial-correctness-checking/9-1-update-2/overview-001.html
Stampede3: https://tacc.utexas.edu/use-tacc/software-list/ Kyric: Latest, 2021.1.1
Stampede-3: 21.9, 22.0
Intel Trace Analyzer and Collector (ITAC) is a performance analysis tool designed for parallel applications. It provides in-depth performance data to help developers optimize the performance of their parallel code.
itk Aces, Faster Image Analysis Library Engineering & Technology Biomedical Imaging Medical & Health Sciences ITK is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
Description Source: https://itk.org/
ITK offers a wide range of tools for image analysis, including image filtering, segmentation, registration, and visualization. It provides support for N-dimensional images and is designed to be extensible, facilitating the integration of new algorithms. Image Processing, Medical Imaging, Scientific Images https://itk.org/ https://docs.itk.org/en/latest/ https://examples.itk.org//
https://github.com/InsightSoftwareConsortium/ScientificImageAnalysisVisualizationAndArtificialIntelligenceCourse
https://itk.org/ItkSoftwareGuide.pdf
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.2.1
Faster: 5.2.1
The Insight Segmentation and Registration Toolkit (ITK) is an open-source, cross-platform library that provides advanced image processing algorithms for registering and segmenting multidimensional scientific images.
ivar Anvil Library Development Computer & Information Sciences Ivar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Ivar allows for easy template creation and usage, supports simple placeholders for data replacement, and offers basic control structures like conditionals and loops. Python Library, Templating Engine, Open-Source Anvil: https://www.rcac.purdue.edu/software/ivar Anvil: 1.3.1, 1.4.2 Ivar is an open-source lightweight templating engine for Python, focused on simplicity and ease of use.
jags Expanse, Faster Statistical Modeling Statistical Analysis Software Mathematics Bayesian Statistics Statistics & Probability JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.
Description Source: https://mcmc-jags.sourceforge.io/
1. Bayesian hierarchical modeling
2. Markov Chain Monte Carlo (MCMC) simulation
3. Model specification
4. Posterior inference
5. Parameter estimation
Bayesian Statistics, Hierarchical Modeling, Mcmc Simulation https://mcmc-jags.sourceforge.io/ https://cran.r-project.org/web/packages/rjags/rjags.pdf https://www.sas.rochester.edu/psc/thestarlab/help/JAGS.pdf Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Expanse: 4.3.0
Faster: 4.3.0
JAGS (Just Another Gibbs Sampler) is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. It is similar to WinBUGS and provides a flexible environment for specifying complex statistical models.
jansson Aces, Faster Data Processing Library Computer & Information Sciences Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite 1. Parsing and generation of JSON data.
2. Supports precise error reporting for debugging.
3. Extendable through custom memory allocation functions.
4. Provides a flexible API for manipulating JSON data structures.
5. High performance and low memory consumption.
Json, C Library, Data Parsing, Data Manipulation Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.13.1
Faster: 2.13.1
Jansson is a C library for encoding, decoding, and manipulating JSON data. It is designed to be efficient, powerful, and easy to use for integrating JSON parsing and generation capabilities into C/C++ applications.
jasper Aces, Expanse, Faster Image Processing Library Computer & Information Sciences Data Compression Computer Science Jasper is an open-source JPEG image codec library that provides encoding and decoding functionality for JPEG images. It is designed for high performance and is commonly used in applications that require image compression and decompression capabilities. 1. Support for encoding and decoding JPEG-2000 images
2. Color space conversion
3. Wavelet transforms
4. Quantization
5. Entropy coding
Image Processing, Open-Source, Jpeg-2000 https://www.ece.uvic.ca/~frodo/jasper/ https://jasper-software.github.io/jasper-manual/latest/html/index.html https://jasper-software.github.io/jasper-manual/latest/html/lib.html#lib_intro
https://jasper-software.github.io/jasper-manual/latest/html/lib_init.html#init_setup_example_1
https://jasper-software.github.io/jasper-manual/latest/html/apps.html#app_intro
Aces: https://hprc.tamu.edu/software/aces/
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.0.24, 2.0.28, 2.0.33, 4.0.0
Expanse: 2.0.16
Faster: 1.900.1, 2.0.14, 2.0.24, 2.0.28, 2.0.33, 4.0.0
JasPer (JPEG-2000 Part-1 Suite) is an open-source software implementation of the JPEG-2000 Part-1 standard. It provides a complete set of tools for encoding and decoding JPEG-2000 streams, including color space conversion, wavelet transforms, quantization, and entropy coding.
java Aces, Faster Compiler Programming Language Computer & Information Sciences Java is a programming language and computing platform first released by Sun Microsystems in 1995. It has evolved from humble beginnings to power a large share of today’s digital world, by providing the reliable platform upon which many services and applications are built. New, innovative products and digital services designed for the future continue to rely on Java, as well.
Description Source: https://www.java.com/en/download/help/whatis_java.html
Java is platform-independent, object-oriented, and has a large standard library. It supports multithreading, garbage collection, and exception handling. Java applications are typically compiled to bytecode that can run on any Java virtual machine (JVM). Programming Language, Computing Platform https://www.oracle.com/java/ https://docs.oracle.com/en/java/javase/22/docs/api/index.html https://docs.oracle.com/javase/tutorial/
https://docs.oracle.com/javase/tutorial/reallybigindex.html
https://www.w3schools.com/java/
https://www.tutorialspoint.com/java/index.htm
https://www.codecademy.com/learn/learn-java
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.8.0_371, 11.0.16, 11.0.18, 17.0.6
Faster: 1.8.0_281, 1.8.0_292-Openjdk, 11.0.2, 13.0.2, 15.0.1, 17.0.2
Java is a widely-used programming language and computing platform that is designed to be fast, secure, and reliable. It is commonly used for building mobile applications, web applications, enterprise applications, and more.
jax Aces, Faster Machine Learning Library Computer & Information Sciences Artificial Intelligence & Intelligent Systems JAX is Autograd and XLA, brought together for high-performance numerical computing, including large-scale machine learning research.
Description Source: https://github.com/google/jax
JAX provides a functional framework that extends NumPy and enables GPU/TPU acceleration, automatic differentiation for Python and NumPy functions, custom vectorizable NumPy functions, composable transformations, and efficient gradient computation. Machine Learning, Numerical Computing, Scientific Computing https://github.com/google/jax https://jax.readthedocs.io/en/latest/ https://jax.readthedocs.io/en/latest/notebooks/quickstart.html
https://jax.readthedocs.io/en/latest/jax-101/index.html
https://jax.readthedocs.io/en/latest/advanced_guide.html
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.2.20, 0.3.25-Cuda-11.7.0, 0.3.25, 0.4.4-Cuda-11.8.0, 0.4.4
Faster: 0.2.19, 0.2.24-Cuda-11.3.1, 0.2.24, 0.3.9-Cuda-11.3.1, 0.3.9, 0.3.23-Cuda-11.7.0
JAX is an open-source software library for high-performance machine learning research, particularly for automatic differentiation, and numerical and scientific computing.
jbigkit Aces, Faster JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. This library is available in portable C code. It is widely used in fax products, printer firmware, printer drivers, document management systems and imaging software.
Description Source: https://www.cl.cam.ac.uk/~mgk25/jbigkit/
https://www.cl.cam.ac.uk/~mgk25/jbigkit/ https://github.com/nu774/jbigkit https://github.com/nu774/jbigkit/tree/master/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.1
Faster: 2.1
jcvi Anvil Analysis Tools Bioinformatics Tools Biological Sciences Genomics Bioinformatics Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. JCVI offers a suite of bioinformatics tools for analyzing biological data, including sequence alignment, assembly, visualization, and annotation. These tools are designed to assist researchers in genomics, metagenomics, transcriptomics, and other areas of computational biology. Bioinformatics, Computational Biology Anvil: https://www.rcac.purdue.edu/software/jcvi Anvil: 1.2.7, 1.3.1 J. Craig Venter Institute (JCVI) software tools for bioinformatics analysis and computational biology.
jdftx Faster Simulation Software Scientific Software Physical Sciences JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. JDFTx is written using highly-templated and object oriented C++11 code in order to express all the physics in the DFT++ algeraic framework [13], while simultaneously maintaining a small memory footprint and supporting a range of hardware architectures (such as GPUs using CUDA) without requiring hand-optimized implementations for each architecture.
Description Source: https://jdftx.org/
Performs Density-Functional Theory Calculations, Supports Joint Density-Functional Theory (Jdft), Allows For Electronic Structure Analysis Of Materials, Includes Features For Simulating Various Physical Properties Computational Software, Electronic Structure Calculations, Materials Science https://jdftx.org/ https://jdftx.org/DevGuide.html https://jdftx.org/Tutorials.html Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.7.0-Cuda-12.2.0, 1.7.0 JDFTx is a computational package for joint density-functional theory (JDFT) calculations. It enables electronic structure calculations for materials using the JDFT formalism, offering a versatile tool for a wide range of research applications.
jdk Darwin Compiler Development Tools Computer & Information Sciences Java Development, Compilation, Documentation Generation, Runtime Environment, Archiving Development Kit, Software Development, Java JDK (Java Development Kit) is a software development environment used for developing Java applications. It includes a Java Runtime Environment (JRE), an interpreter/loader (Java), a compiler (javac), an archiver (jar), a documentation generator (Javadoc), and some other tools needed in Java development.
jellyfish Expanse Bioinformatics Tool Computational Biology Biological Sciences Jellyfish is a fast and memory-efficient software for counting k-mers in DNA sequences, which are commonly used in genome analysis and sequence assembly. It provides algorithms for k-mer counting, storage, and querying to extract valuable insights from biological data. 1. Counting k-mers in DNA sequences
2. Memory-efficient data storage
3. Fast querying of k-mer counts
4. Support for large sequencing datasets
K-Mer Counting, DNA Sequences, Sequence Analysis https://www.genome.umd.edu/jellyfish.html https://github.com/gmarcais/Jellyfish/tree/master/doc https://github.com/gmarcais/Jellyfish/tree/master/examples
https://github.com/gmarcais/Jellyfish/tree/master#usage
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules Expanse: Xvw2Ec7 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA sequences. It has the capability to efficiently store and query k-mer counts in large sequencing datasets.
jemalloc Aces, Faster Memory Allocator Library Computer & Information Sciences jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. Efficient Memory Allocation & Deallocation, Optimized For Multithreaded Applications, Scalable & Customizable, Supports Advanced Memory Management Features Memory Allocator, Performance Optimization, Multithreading Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 5.2.1
Faster: 5.2.1
jemalloc is a general-purpose memory allocator implementation designed for high performance in multithreaded applications. It is widely used in the software industry to optimize memory allocation and improve overall performance of applications.
jmol Aces Modeling & Simulation Visualization Chemical Sciences Chemical Sciences Physical Chemistry, Inorganic & Nuclear Chemistry Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules Jmol allows users to view 3D chemical structures, display crystal structures, visualize protein structures, animate molecules, and perform measurements and analysis on molecular structures. It supports a wide range of file formats for input and output, including CIF, PDB, XYZ, and more. Users can customize the display of molecules with various rendering options, color schemes, and labeling. Molecular Visualization, Molecular Analysis, Chemistry Aces: https://hprc.tamu.edu/software/aces/ Aces: 16.1.59-Java-1.8.0_371, 16.1.59 Jmol is an open-source Java viewer for chemical structures in 3D with features for visualization, analysis, and manipulation of molecular structures.
json-c Aces, Faster, Kyric Data Processing Library Computer & Information Sciences Software Engineering, Systems, & Development Computer Science JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects. It aims to conform to RFC 7159.
Description Source: https://github.com/json-c/json-c/wiki
Parsing Json Input, Creating Json Output, Manipulating Json Data Structures, Validating Json Data C Library, Json Encoding, Json Decoding, Data Manipulation https://github.com/json-c/json-c https://json-c.github.io/json-c/json-c-0.17/doc/html/index.html https://github.com/json-c/json-c/wiki/List-of-json-c-tutorials Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 0.16
Faster: 0.16
Json-c is a C library for encoding, decoding, and manipulating JSON data. It provides functions for parsing JSON input, creating JSON output, manipulating JSON data structures, and validating JSON data.
jsoncpp Aces, Faster Development Tools Library Computer & Information Sciences JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
Description Source: https://github.com/open-source-parsers/jsoncpp
Parsing Json Data, Generating Json Data, Manipulating Json Data Structures, Support For C++ Applications C++, Json, Library, Data Manipulation https://github.com/open-source-parsers/jsoncpp https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html https://github.com/open-source-parsers/jsoncpp/wiki#code-example
https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html#_example
https://github.com/open-source-parsers/jsoncpp/tree/master/example
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 1.9.4, 1.9.5
Faster: 1.9.3, 1.9.4, 1.9.5
JsonCpp is a C++ library that allows manipulating JSON data structures. It provides features for parsing, generating, and manipulating JSON data in C++ applications.
judy Faster Data Management Library Other Computer & Information Sciences Some core features of Judy include high performance, memory efficiency, scalability with large data sets, support for dynamic arrays, and a simple API for easy integration. C Library, Data Management, Key/Value Pairs Faster: https://hprc.tamu.edu/software/faster/ Faster: 1.0.5 Judy is a C library that provides a collection of functions to efficiently manage data arrays to store and retrieve key/value pairs.
julia Aces, Anvil, Bridges-2, Darwin, Delta, Expanse, Faster, Ookami Compiler Programming Language Computer & Information Sciences Julia is a general purpose high-performance flexible programming language which can be used to write any application. It is well-suited for scientific and numerical computing.
Description Source: https://julialang.org/
Julia combines the high-level ease of use and flexibility of languages like Python and Matlab with the speed and performance of lower-level languages like C and Fortran. It offers a just-in-time compiler that generates optimized machine code using LLVM, making it highly efficient for numerical and scientific computing. Julia supports multiple dispatch, which allows functions to be defined with multiple methods with different argument types or numbers. It also has built-in package manager and a vast ecosystem of packages for various domains such as data science, machine learning, optimization, and more. Programming Language, Technical Computing, High-Performance Computing, Scientific Computing, Numerical Analysis https://julialang.org/ https://docs.julialang.org/en/v1/ https://juliaacademy.com/courses/
https://www.youtube.com/user/JuliaLanguage/playlists
https://julialang.org/learning/tutorials/
https://julialang.org/learning/notebooks/
Aces: https://hprc.tamu.edu/software/aces/
Anvil: https://www.rcac.purdue.edu/software/julia
Bridges-2: https://www.psc.edu/resources/software/julia
Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Faster: https://hprc.tamu.edu/software/faster/
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Aces: 1.8.5-Linux-X86_64, 1.9.3-Linux-X86_64, 1.10.0-Musl-X86_64, 1.10.2-Linux-X86_64
Anvil: V2.4.2, 1.6.2
Bridges-2: 1.5.2
Delta: 1.9.0, 1.10.2
Expanse: Olutp43
Faster: 1.6.5-Linux-X86_64, 1.7.0-Linux-X86_64, 1.7.1-Linux-X86_64, 1.7.2-Linux-X86_64, 1.8.0-Linux-X86_64, 1.9.3-Linux-X86_64
Ookami: 1.8.3
Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments. It provides a sophisticated compiler, distributed parallel execution, numerical accuracy, and extensive mathematical function libraries.
junit Faster Development Tool Software Testing Framework Computer & Information Sciences Software Development Software Engineering, Systems, & Development Supports Writing & Running Automated Tests In Java, Provides Annotations For Test Methods, Includes Assertion Methods For Test Results, Supports Test Fixtures To Set Up Initial Conditions, Generates Test Reports For Easy Result Analysis Unit Testing, Java, Testing Framework Faster: https://hprc.tamu.edu/software/faster/ Faster: 4.12-Java-1.8 JUnit is a popular open-source unit testing framework for Java programming language. It is widely used by developers to write and run repeatable automated tests to ensure the correctness of their code.
jupyter Anvil, Jetstream, Ookami Web Application Computational Notebook Computer & Information Sciences JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning. Interactive Computing, Data Visualization, Collaborative Notebooks, Support For Multiple Programming Languages Data Science, Scientific Computing, Machine Learning https://jupyter.org/ https://docs.jupyter.org/en/latest/ https://docs.jupyter.org/en/latest/use/using.html
https://docs.jupyter.org/en/latest/start/index.html
Anvil: https://www.rcac.purdue.edu/software/jupyter
Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami
Anvil: 2.0.0
Ookami: Latest
Jupyter is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. It supports over 40 programming languages, including Python, R, and Julia, and is widely used in data science, scientific computing, and machine learning projects.
jupyter-notebook Ookami Ookami: https://www.stonybrook.edu/commcms/ookami/support/faq/software_on_ookami Ookami: 7.0.6
jupyter-server Aces Compiler Computational Software Computer & Information Sciences The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila. Web-Based Interface, Interactive Computational Environments, Support For Multiple Programming Languages Interactive Computing, Web-Based Interface, Notebooks Aces: https://hprc.tamu.edu/software/aces/ Aces: 2.7.0, 2.7.2 Jupyter server is a flexible and extensible tool that allows users to run interactive computational environments in various programming languages. It provides a web-based interface for running Jupyter notebooks, code, and data analysis.
jupyterhub Jetstream Collaborative Tool Data Science Tools Computer & Information Sciences Data Science Informatics, Analytics & Information Science JupyterHub brings the power of notebooks to groups of users. It gives users access to computational environments and resources without burdening the users with installation and maintenance tasks. Multi-User Jupyter Notebook Server, Browser-Based Interface, Support For Multiple Languages Including Python, R, & Julia, Scalability For Large Groups Of Users, Customizable User Environments, Integration With Authentication Services Like Oauth & Ldap Data Science, Collaborative Computing, Notebook Environment, Interactive Computing https://jupyter.org/hub https://jupyterhub.readthedocs.io/en/stable/ https://jupyterhub.readthedocs.io/en/stable/tutorial/index.html
https://jupyterhub.readthedocs.io/en/stable/howto/index.html
https://github.com/jupyterhub/jupyterhub-tutorial
JupyterHub brings the power of Jupyter Notebooks to groups of users. It allows multiple users to access Jupyter Notebooks through a browser, providing a collaborative and interactive environment for data science, scientific computing, and other computational tasks.
jupyterlab Aces, Jetstream Data Science Tool Integrated Development Environment (Ide) Computer & Information Sciences JupyterLab is the latest web-based interactive development environment for notebooks, code, and data. Its flexible interface allows users to configure and arrange workflows in data science, scientific computing, computational journalism, and machine learning. Web-Based Interface For Interactive Computing, Support For Jupyter Notebooks, Text Editors, Terminals, & Custom Components, Integration With Data Visualization Libraries & Tools, Ability To Work With Multiple Programming Languages Like Python, R, & Julia, Customizable User Interface With Drag-&-Drop Features, Interactive Widgets For Data Exploration & Visualization Interactive Computing, Data Visualization, Jupyter Notebooks, Web-Based Interface, Code Editing https://github.com/jupyterlab/jupyterlab https://jupyterlab.readthedocs.io/en/stable/user/index.html https://jupyterlab.readthedocs.io/en/stable/getting_started/overview.html
https://www.youtube.com/watch?v=7wfPqAyYADY
Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.0.3 JupyterLab is a web-based interactive development environment for Jupyter notebooks, code, and data. It offers a flexible and powerful user interface to work with data, code, and visualization in a seamless manner.
jupyterlmod Aces Extension Environment Management Other Natural Sciences Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod's Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc. Integration Of Lmod With Jupyter Notebooks, Software Environment Management, Module Loading & Unloading, Environment Variable Handling Jupyter Notebook, Environment Modules, Software Environment Management Aces: https://hprc.tamu.edu/software/aces/ Aces: 4.0.3 jupyterlmod is an extension for Jupyter Notebooks that allows users to interact with Lmod, the Environment Modules System, directly within the Jupyter environment. It enables users to manage software environments, load and unload modules, and handle environment variables conveniently within Jupyter Notebook.
jupyternotebook Aces The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. Aces: https://hprc.tamu.edu/software/aces/ Aces: 7.0.3
kahip Aces, Faster Utility Algorithm Computer & Information Sciences Computer Science KaHIP - Karlsruhe High Quality Partitioning - is a family of graph partitioning programs. It includes KaFFPa (Karlsruhe Fast Flow Partitioner), which is a multilevel graph partitioning algorithm, in its variants Strong, Eco and Fast, KaFFPaE (KaFFPaEvolutionary) which is a parallel evolutionary algorithm that uses KaFFPa to provide combine and mutation operations, as well as KaBaPE which extends the evolutionary algorithm. Moreover, specialized techniques are included to partition road networks (Buffoon), to output a vertex separator from a given partition or techniques geared towards efficient partitioning of social networks.
Description Source: https://kahip.github.io/
Efficient Computation Of High-Quality Graph Partitions, Multiple Partitioning Algorithms, Optimization For Load Balancing & Communication Reduction, Suitable For Large-Scale Parallel Applications Graph Partitioning, High-Performance Computing, Parallel Computing https://kahip.github.io/ https://github.com/KaHIP/KaHIP https://github.com/KaHIP/KaHIP/tree/master/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.14, 3.16
Faster: 3.14
KaHIP (Karlsruhe High Quality Partitioning) is a family of graph partitioning programs that aims to efficiently compute high-quality graph partitions. It provides several partitioning algorithms to balance computational load and minimize communication overhead. KaHIP is suitable for large-scale parallel applications and is widely used in the field of high-performance computing.
kaiju Anvil Sequence Analysis Tool Bioinformatics Tool Biological Sciences Bioinformatics Biological Sciences Kaiju is a tool for fast taxonomic classification of metagenomic sequencing reads using a protein reference database. Taxonomic Classification Of DNA Sequences, High Accuracy In Assigning Taxonomic Labels, Utilizes Burrows-Wheeler Transform & Fm-Index, Designed For High-Throughput Sequencing Reads Bioinformatics, Computational Biology, Genomics, Sequencing Data Anvil: https://www.rcac.purdue.edu/software/kaiju Anvil: 1.8.2 Kaiju is a program for the taxonomic classification of high-throughput sequencing reads. It assigns taxonomic labels to short DNA sequences with near-perfect accuracy. Kaiju is based on the Burrows-Wheeler transform (BWT) and the FM-index. It has been designed to analyze sequencing reads generated by high-throughput sequencing technologies, such as Illumina, Pacific Biosciences, and Ion Torrent.
kakscalculator2 Anvil Tool Mathematical Calculation Mathematics kakscalculator2 is a toolkit of incorporating gamma series methods and sliding window strategies. 1. Advanced mathematical calculations
2. User-friendly interface
3. Efficient computation of complex problems
4. Mathematical modeling capabilities
Mathematics, Software, Computation Anvil: https://www.rcac.purdue.edu/software/kakscalculator2 Anvil: 2.0.1 kakscalculator2 is a software tool designed for performing advanced mathematical calculations and computations. It provides a user-friendly interface for solving complex mathematical problems efficiently.
kalign Aces, Faster Bioinformatics Tool Algorithm Biological Sciences Kalign is a fast multiple sequence alignment program for biological sequences.
Description Source: https://github.com/TimoLassmann/kalign
Fast & Accurate Multiple Sequence Alignment, Utilizes The Wu-Manber Approximate String Matching Algorithm, Suitable For Aligning Large Sets Of Sequences, Supports DNA, RNA, & Protein Sequences Bioinformatics, Sequence Alignment, DNA, RNA, Protein, Wu-Manber Algorithm https://github.com/TimoLassmann/kalign/blob/main/doc/paper/kalign3.org https://github.com/TimoLassmann/kalign https://github.com/TimoLassmann/kalign#examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 3.3.1, 3.3.5, 3.4.0
Faster: 3.3.1
Kalign is a fast and accurate multiple sequence alignment algorithm that utilizes the Wu-Manber approximate string matching algorithm to efficiently align large sets of sequences. It is commonly used in bioinformatics for aligning DNA, RNA, and protein sequences.
kallisto Anvil, Expanse Bioinformatics Tool Quantification Tool Biological Sciences Transcriptomics Bioinformatics Kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. Efficient & Ultrafast RNA-Seq Quantification, Pseudoalignment-Based Approach, Accurate & Reliable Transcript Quantification, Compatibility With Standard RNA-Seq Analysis Pipelines, Multiple Output Formats For Downstream Analysis RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology Anvil: https://www.rcac.purdue.edu/software/kallisto
Expanse: https://www.sdsc.edu/support/user_guides/expanse.html#modules
Anvil: 0.46.2, 0.48.0
Expanse: Bdaqnwj
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, using pseudoalignment to quickly determine compatibility of reads with targets, allowing rapid transcript quantification.
kblas-gpu Aces Computational Software Numerical Library Engineering & Technology KAUST BLAS (KBLAS) is a high performance CUDA library implementing a subset of BLAS as well as Linear Algebra PACKage (LAPACK) routines on NVIDIA GPUs. 1. Accelerated linear algebra operations on NVIDIA GPUs. 2. Optimized Basic Linear Algebra Subroutines (BLAS) for high-performance computing. 3. Dense matrix operations such as matrix-matrix multiplication, matrix-vector multiplication, etc. 4. Support for various data types and precision levels. 5. High-performance and parallel computation capabilities. Linear Algebra, Gpu-Accelerated, Hpc, Parallel Computing Aces: https://hprc.tamu.edu/software/aces/ Aces: 20231024-Cuda-11.8.0 KBLAS is a GPU-accelerated linear algebra library for high-performance computing (HPC) applications. It provides optimized implementations of basic linear algebra subroutines (BLAS) and dense matrix operations for NVIDIA GPUs.
kbproto Delta Protocol Library Computer & Information Sciences Computer Science Computer Science 1. Provides XKB protocol and extension definitions. 2. Allows for usage with X11 protocol libraries. 3. Defines keyboard properties and types for X Window System. X11 Protocol, Keyboard Properties Delta: https://docs.ncsa.illinois.edu/systems/delta/en/latest/user_guide/software.html Delta: 1.0.7 The kbproto package provides the core XKB protocol and extension definitions for usage with X11 protocol libraries.
kcachegrind Darwin Visualization Tool Development Tools Computer & Information Sciences Visualize Profiling Data, Identify Performance Bottlenecks, Interact With Call Graphs & Call Trees, View Cache Utilization & Branch Prediction Performance Analysis, Software Profiling, Software Visualization KCacheGrind is a visualisation tool that allows to profile data and identify performance bottlenecks in software applications. It is commonly used for analyzing profiling data generated by Cachegrind and Callgrind.
kentutils Anvil Bioinformatics Tools Utility Biological Sciences Genomics, Computational Biology Bioinformatics Kentutils: UCSC command line bioinformatic utilities. 1. Utilities for manipulating genomic data.
2. Tools for analyzing genome sequences.
3. Support for various file formats commonly used in genomics.
Genomics, Genome Browser, Utilities Anvil: https://www.rcac.purdue.edu/software/kentutils Anvil: 302.1.0 kentutils is a collection of utilities provided by the UCSC Genome Browser that allow for the manipulation and analysis of genomic data. These tools are particularly useful for researchers working with genomics data and looking to perform various operations on genome sequences.
keras Aces, Faster Library Neural Network Library Computer & Information Sciences Machine Learning Artificial Intelligence & Intelligent Systems Keras is a deep learning API written in Python and capable of running on top of either JAX, TensorFlow, or PyTorch.
Description Source: https://keras.io/about/
1. User-friendly API
2. Modular and extensible
3. Supports both convolutional networks and recurrent networks, as well as combinations of the two
4. Runs seamlessly on CPU and GPU
Neural Networks, Deep Learning, Machine Learning https://keras.io/ https://keras.io/api/ https://www.tensorflow.org/guide/keras
https://keras.io/getting_started/intro_to_keras_for_engineers/
https://keras.io/examples/
Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.4.3-Tensorflow-2.5.0
Faster: 2.4.3
Keras is an open-source neural network library written in Python. It is capable of running on top of TensorFlow, Microsoft Cognitive Toolkit, Theano, or PlaidML. Designed with user-friendliness and modularity as its guiding principles, Keras is known for its ease of use and flexibility, allowing users to experiment with deep neural networks.
khmer Anvil Bioinformatics Tool Research Tools Biological Sciences Khmer is a tool for k-mer counting, filtering, and graph traversal FTW! K-Mer Counting, Data Trimming & Error-Trimming, Digital Normalization Of Reads, Partitioning Large Data Sets Bioinformatics, Hpc Tools, Computational Software Anvil: https://www.rcac.purdue.edu/software/khmer Anvil: 3.0.0A3 Khmer is a set of tools for working with DNA sequence data that is extremely efficient both in terms of speed and memory consumption. It is designed to pre-process sequencing data to reduce the memory requirements of de Bruijn graph based assemblers for metagenome data. The tools can be used for counting k-mers and finding k-mers that occur many times, trimming and error-trimming data, digital normalization of reads, and partitioning large data sets.
kim-api Aces, Faster Application Programming Interface Simulation Tools Physical Sciences Materials Simulation Materials Science The Knowledgebase of Interatomic Models (KIM) Application Programming Interface (API) defines a standard (the Portable Model Interface (PMI)) for how molecular simulators interface with interatomic models (also called potentials or force-fields). This allows a single computer implementation of a Portable Model (PM) to be used without modification within multiple simulator codes. A PM can include code and parameters all in one. Or, a PM can include just parameters and use a separate Model Driver (MD) library containing the code.
Description Source: https://openkim.org/kim-api/
1. Standardizes the interface between atomistic simulation codes and interatomic potential models.
2. Enables the seamless integration of new potential models into existing simulation codes.
3. Facilitates the sharing and dissemination of interatomic models within the materials science community.
4. Supports multiple programming languages, including C/C++, Fortran, Python, and MATLAB.
Computational Software, Hpc Tools https://openkim.org/kim-api/ https://kim-api.readthedocs.io/en/latest/ https://github.com/openkim/kim-api/tree/master/examples Aces: https://hprc.tamu.edu/software/aces/
Faster: https://hprc.tamu.edu/software/faster/
Aces: 2.2.1, 2.3.0
Faster: 2.1.3, 2.2.1, 2.3.0
The Knowledgebase for Interatomic Models (KIM) Application Programming Interface (API) is an open framework for the development of interoperable atomistic and multiscale simulation codes. It provides a common interface for atomistic simulations and facilitates the incorporation and sharing of interatomic models.
kineto Aces Analysis Tool Simulation Engineering & Technology Mechanical Engineering Engineering & Technology kineto is a CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters.
Description Source: https://github.com/pytorch/kineto
Kinematic Analysis Of Mechanical Systems, Dynamic Analysis Of Mechanical Systems, Simulation Of Rigid Body Motion With Joints & Constraints, Visualization Of Motion & Forces In Mechanical Systems Mechanical Engineering, Simulation, Mechanical Systems, Kinematics, Dynamics https://github.com/pytorch/kineto https://github.com/pytorch/kineto/blob/main/libkineto/README.md https://github.com/pytorch/kineto/tree/main/libkineto/sample_programs Aces: https://hprc.tamu.edu/software/aces/ Aces: 0.4.0 Kineto is a software suite designed for analyzing and simulating the dynamics of mechanical systems. It provides tools for both kinematic and dynamic analysis of systems with rigid bodies, joints, and constraints. Kineto is particularly useful for studying the motion and forces in complex mechanical systems.
kissde Anvil Bioinformatics Tool Simulation Tool Biological Sciences Synthetic Biology, Systems Biology Biological Sciences kissDE is a R package, similar to DEseq, but which works on pairs of variants, and tests if a variant is enriched in one condition. Simulation Of Gene Expression Dynamics, Modeling Protein Degradation Kinetics, Optimization Of Synthetic Genetic Circuits, Analysis Of Synthetic Biological Systems Computational Biology, Bioinformatics Anvil: https://www.rcac.purdue.edu/software/kissde Anvil: 1.15.3 KISSDE (Kinetic Simulator of Synthetic Degradation and Expression) is a software tool for simulating the kinetics of gene expression and protein degradation in synthetic biological systems. It allows users to model the dynamics of gene expression and protein degradation processes to better understand and optimize synthetic genetic circuits.
kissplice Anvil Bioinformatics Tool Analysis Tool Biological Sciences Transcriptomics Bioinformatics KisSplice is a software that enables to analyse RNA-seq data with or without a reference genome. Identification Of Various RNA Splicing Events, Quantification Of Splicing Events, Visualization Of Splicing Patterns, Detection Of Novel Splicing Events, Analysis Of Alternative Splicing Dynamics Bioinformatics, RNA-Seq, Splicing, Transcriptomics Anvil: https://www.rcac.purdue.edu/software/kissplice Anvil: 2.6.2 Kissplice is a bioinformatics tool designed for the analysis of RNA-Seq data to identify and quantify various types of RNA splicing events such as exon skipping, intron retention, and alternative 5' or 3' splicing.
kissplice2refgenome Anvil RNA-Seq Analysis Tool Bioinformatics Tool Biological Sciences Gene Expression Analysis Genetics, Bioinformatics KisSplice can also be used when a reference (annotated) genome is available, in order to annotate the variants found and help prioritize cases to validate experimentally. In this case, the results of KisSplice are mapped to the reference genome, using for instance STAR, and the mapping results are analysed using KisSplice2RefGenome. 1. Alignment of RNA-Seq reads to a reference genome.
2. Detection of fusions and alternative splicing events.
3. Identification of various types of splicing events like exon skipping and intron retention.
4. Provides detailed reports and visualizations for the detected events.
Computational Biology, RNA-Seq Analysis, Splice Junction Detection Anvil: https://www.rcac.purdue.edu/software/kissplice2refgenome Anvil: 2.0.8 Kissplice2refgenome is a computational tool used for the detection of fusions and alternative splicing events in RNA-Seq data. It aligns reads on a reference genome and detects different types of events including fusions, exon skipping, intron retention, and more.
kma Anvil Analysis Tool Alignment Tool Biological Sciences Genomics Bioinformatics KMA is a mapping method designed to map raw reads directly aga