Explore software available on ACCESS Resources.
| Software | Installed on | AI Description | AI Tags | AI Research Discipline | AI Software Type | Documentation, Uses, and more |
|---|---|---|---|---|---|---|
| 7z | Ookami | 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. | File Archiver, Compression, Encryption | General | Archiver | Documentation, Uses, and more |
| abaqus | Expanse FASTER |
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. | Simulation, Finite Element Analysis, Computer-Aided Engineering, Materials Analysis | Engineering & Technology | Simulation Software | Documentation, Uses, and more |
| abinit | Bridges-2 FASTER |
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. | Materials Science, Condensed Matter Physics, Electronic Structure Calculations | Condensed Matter Physics, Physical Sciences | Electronic Structure Calculation | Documentation, Uses, and more |
| abricate | FASTER | abricate is a tool for finding antimicrobial resistance and virulence genes in bacterial genomes. | Antimicrobial Resistance, Genomic Analysis, Bacterial Genomics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| abseil | ACES FASTER |
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. | C++ Library, Open Source, Cross-Platform | General, Computer & Information Sciences | Code Library | Documentation, Uses, and more |
| absl-py | ACES FASTER |
Documentation, Uses, and more | ||||
| abyss | ACES Bridges-2 FASTER |
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. | Assembly, De Novo Assembly, Sequence Assembler, Large Genomes | Biological Sciences | Hpc Tool | Documentation, Uses, and more |
| accelerate | ACES FASTER |
Documentation, Uses, and more | ||||
| actc | ACES FASTER |
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. | Graph Analytics, Connected Components, Distributed Computing | Biology, Mathematics, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| adapterremoval | FASTER | 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. | Bioinformatics, Hts Data Processing, Sequence Analysis | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| adept-2 | FASTER | Documentation, Uses, and more | ||||
| adios2 | ACES Stampede3 |
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. | I/O Middleware, High-Performance Computing, Data Management, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| admixture | FASTER | Documentation, Uses, and more | ||||
| advisor | KyRIC Stampede3 |
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. | Hpc, Performance Optimization, Parallel Computing | Engineering & Technology | Performance Optimization | Documentation, Uses, and more |
| aesara | FASTER | 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. | Python Library, Symbolic Computation, Deep Learning, Optimization | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| aflow | FASTER | 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. | Computational Software, Materials Science, Density Functional Theory | Physics & Physical Sciences, Physical Sciences | Materials Modeling & Simulation | Documentation, Uses, and more |
| agat | FASTER | AGAT (Annotation-based Genome Assembly Toolkit) is a pipeline designed for comprehensive annotation and evaluation of genome assemblies. | Genome Assembly, Annotation, Evaluation, Genomic Analysis | Genomics, Biological Sciences | Pipeline | Documentation, Uses, and more |
| agent | FASTER | Documentation, Uses, and more | ||||
| ai-tools-gpu | ACES | Documentation, Uses, and more | ||||
| aiohttp | ACES FASTER |
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. | Python Library, Web Development, Asynchronous Programming | Computer & Information Sciences | Http Client/Server Framework | Documentation, Uses, and more |
| alitv | FASTER | Documentation, Uses, and more | ||||
| aliview | FASTER | Documentation, Uses, and more | ||||
| allhic | FASTER | Documentation, Uses, and more | ||||
| alphafold | ACES FASTER |
AlphaFold is a deep learning-based system developed by DeepMind to predict protein folding and 3D structure with high accuracy. | Protein Folding, Structure Prediction, Deep Learning, Neural Networks | Bioinformatics, Biological Sciences | Web Application | Documentation, Uses, and more |
| alphafold3 | ACES FASTER |
Documentation, Uses, and more | ||||
| alphapickle | ACES FASTER |
Alphapickle is a Python library that provides tools and utilities for working with alpha factors and optimizing portfolio construction in quantitative finance. | Python Library, Quantitative Finance, Alpha Factors, Portfolio Optimization | Financial Engineering, Other Mathematics | Data Analysis | Documentation, Uses, and more |
| alphapulldown | ACES | Documentation, Uses, and more | ||||
| alsa-lib | ACES FASTER |
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. | Linux, Audio, Library | Computer & Information Sciences | Audio Library | Documentation, Uses, and more |
| amask | Stampede3 | 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. | Molecular Visualization, Atomic Structures, Molecular Modeling, Research Tool | Biological Sciences | Molecular Visualization Software | Documentation, Uses, and more |
| amber | ACES Anvil FASTER |
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. | Molecular Dynamics, Biomolecular Simulations, Quantum Chemistry | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics | Documentation, Uses, and more |
| ambertools | ACES Bridges-2 FASTER |
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. | Molecular Dynamics, Computational Chemistry, Biomolecular Structure, Energy Minimization | Biophysics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| amd uprof | Anvil | Documentation, Uses, and more | ||||
| amdblis | Anvil | Amdblis is a computational software for analyzing and visualizing single-molecule data, particularly for biophysical studies. | Computational Software, Data Analysis, Visualization | Biophysics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| amdfftw | Anvil | 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/ |
Mathematics | Library | Documentation, Uses, and more | |
| amdlibflame | Anvil | 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. | Linear Algebra, Numerical Computations, Performance Optimization | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| amdlibm | Anvil | 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. | Mathematics, Numerical Computation, Math Library | Mathematics, Engineering & Technology | Math Library | Documentation, Uses, and more |
| amdscalapack | Anvil | 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. | Mathematics | Library | Documentation, Uses, and more | |
| amduprof | Delta Expanse |
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. | Gpu Profiling, Opencl Profiler, Performance Analysis | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| amos | FASTER | 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. | Assembly, DNA Sequencing, Bioinformatics | Genetics, Biological Sciences | Sequence Assembly Software | Documentation, Uses, and more |
| amphora2 | FASTER | 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. | Bioinformatics, Metagenomics, Phylogenetics | Biological Sciences | Computational Software | Documentation, Uses, and more |
| amplpy | FASTER | Documentation, Uses, and more | ||||
| anaconda | Anvil Jetstream2 Ookami |
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. | Data Science, Scientific Computing, Package Management, Python, R | Informatics, Analytics & Information Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| anaconda2 | Bridges-2 | 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. | Python Libraries, Conda Packages, Data Science, Scientific Computing, Machine Learning, Computational Software | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Distribution | Documentation, Uses, and more |
| anaconda3 | ACES Bridges-2 Delta Expanse FASTER |
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. | Python, Data Science, Machine Learning, Deep Learning, Package Management | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| angsd | FASTER | angsd is a software for analyzing Next Generation Sequencing (NGS) data such as genome-wide association studies (GWAS) and population genomics data. | Ngs Data Analysis, Genome-Wide Association Studies, Population Genomics, Genetic Variation | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| anicalculator | ACES FASTER |
Documentation, Uses, and more | ||||
| annosine | FASTER | Documentation, Uses, and more | ||||
| annovar | ACES FASTER |
ANNOVAR is a powerful software tool designed to annotate genetic variants detected from diverse genomes. | Genomics, Genetic Variation, Bioinformatics, Annotation | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ansys | Bridges-2 FASTER Stampede3 |
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. | Engineering, Simulation, Product Design | Mechanical Engineering, Engineering & Technology | Engineering Simulation Software | Documentation, Uses, and more |
| ansysem | FASTER | Documentation, Uses, and more | ||||
| ant | ACES FASTER |
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. | Automation, Java, Build Tool, Deployment | Computer Science | Tool | Documentation, Uses, and more |
| antlr | ACES FASTER |
ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. | Compiler, Parser Generator, Syntax Analysis, Code Generation | Toolkit | Documentation, Uses, and more | |
| anvi'o | Bridges-2 | Documentation, Uses, and more | ||||
| any2fasta | FASTER | 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. | Sequence Data, Fasta Format, Bioinformatics | Biological Sciences, Natural Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| aocc | ACES Anvil Bridges-2 Delta Expanse FASTER Jetstream2 Ookami |
The AMD Optimizing C/C++ Compiler (AOCC) is a high performance compiler suite with support for C, C++, and Fortran programming languages. | Compiler, C, C++, Fortran, Optimization | Computer & Information Sciences | Service | Documentation, Uses, and more |
| aocl | Bridges-2 | 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. | Fpga, Opencl, Acceleration | Mathematics, Engineering & Technology | Compiler | Documentation, Uses, and more |
| apbs | ACES | Documentation, Uses, and more | ||||
| apptainer | Jetstream2 Stampede3 |
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. | Containerization, Application Management, Devops, Software Development | Engineering & Technology | Development | Documentation, Uses, and more |
| apr | ACES FASTER |
The Apache Portable Runtime (APR) is a software library that provides a predictable and consistent interface to underlying platform-specific implementations. | Software Library, Cross-Platform Development, Operating System Abstraction | Engineering & Technology | Development | Documentation, Uses, and more |
| apr-util | ACES FASTER |
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. | Utility Library, Apache Portable Runtime, Support Library, Additional Features | Library | Documentation, Uses, and more | |
| aragorn | FASTER | Documentation, Uses, and more | ||||
| arcade-learning-environment | FASTER | 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. | Artificial Intelligence | Framework | Documentation, Uses, and more | |
| archive-zip | FASTER | 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. | Python Library, Zip Archives, Compression, Decompression | Application | Documentation, Uses, and more | |
| archspec | ACES FASTER |
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. | Architecture Detection, System Analysis, Performance Optimization, Code Generation | Computer & Information Sciences | Framework | Documentation, Uses, and more |
| arcs | FASTER | 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. | Hpc, Computational Workflows, Data Analysis | Biology, Engineering & Technology | Research Software | Documentation, Uses, and more |
| argobots | ACES | Documentation, Uses, and more | ||||
| argtable | FASTER | Documentation, Uses, and more | ||||
| aria2 | ACES Expanse FASTER |
aria2 is a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. | Download Manager, Command-Line Tool, Multi-Protocol, Multi-Source, File Transfer | Computer & Information Sciences, Other Computer & Information Sciences | Download Manager | Documentation, Uses, and more |
| arm | Ookami | 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. | Software Development, Embedded Applications, Debugging, Performance Optimization | Engineering & Technology | Compiler/Debugger | Documentation, Uses, and more |
| arm-forge | Expanse | 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. | Toolkit | Documentation, Uses, and more | ||
| arm-gnu-toolchain | ACES | 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. | Compiler, Embedded Systems, Arm Processor, Toolchain | Engineering & Technology | Compiler | Documentation, Uses, and more |
| arm-gnu-toolchaint | ACES | Documentation, Uses, and more | ||||
| arm-modules | Ookami | Documentation, Uses, and more | ||||
| armadillo | ACES Delta FASTER |
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. | Linear Algebra, C++ Library | Computer Science, Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| arpack | Stampede3 | 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. | Computational Software, Linear Algebra, Eigenvalue Problems | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| arpack-ng | ACES Anvil FASTER |
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. | Linear-Algebra, Eigenvalue Problems, Sparse Matrices, Iterative Methods, Computational Physics, Computational Chemistry, Fortran | Mathematics, Physical Sciences | Library | Documentation, Uses, and more |
| arriba | Bridges-2 | 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. | Software, Gene Fusion Detection, RNA-Seq, Transcriptome Analysis | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| arrow | ACES FASTER |
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. | Data Processing, Data Analytics, In-Memory Data, Standardized Format | Memory Efficiency, Computer & Information Sciences | Development Platform | Documentation, Uses, and more |
| arrow-r | ACES FASTER |
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. | Statistical Computing, Data Visualization, Statistical Modeling, R Programming | Statistics & Probability, Mathematics | Statistical Software | Documentation, Uses, and more |
| arviz | FASTER | 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. | Python Library, Bayesian Inference, Data Visualization | Statistics & Probability, Other Mathematics | Python Library | Documentation, Uses, and more |
| asciinema | Bridges-2 | 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. | Terminal Recording, Web Sharing, Cli Tool | Computer & Information Sciences | Terminal Recorder | Documentation, Uses, and more |
| ase | ACES FASTER |
Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations. | Computational Software, Python Library, Molecular Simulations | Chemistry, Other Natural Sciences | Tool | Documentation, Uses, and more |
| aspera connect | Bridges-2 | Documentation, Uses, and more | ||||
| assemblytics | FASTER | Documentation, Uses, and more | ||||
| assimp | ACES FASTER |
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 | 3D Models, Asset Import, Game Development | File Loading, Computer & Information Sciences | 3D Modeling/Rendering | Documentation, Uses, and more |
| astropy | FASTER | 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. | Python Library, Astronomy, Astrophysics, Astronomical Research, Data Analysis | Astronomy & Planetary Sciences, Physical Sciences | Computational Software | Documentation, Uses, and more |
| at-spi2-atk | ACES FASTER |
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. | Assistive Technology, Accessibility, User Interface | General, Computer & Information Sciences | Interface | Documentation, Uses, and more |
| at-spi2-core | ACES FASTER |
AT-SPI (Assistive Technology Service Provider Interface) is a protocol that allows assistive technologies to interact with and control applications. | Accessibility, Assistive Technology, Gui Applications | General, Computer Science | Library | Documentation, Uses, and more |
| atk | ACES FASTER |
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. | Computational Chemistry, Materials Science, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Simulation Software | Documentation, Uses, and more |
| atomeye | FASTER | Documentation, Uses, and more | ||||
| atop | Delta | 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. | System Monitor, Performance Analysis, Resource Utilization, Process Activity, System Statistics | General, Computer & Information Sciences | System Monitoring Tool | Documentation, Uses, and more |
| atp | Delta DeltaAI |
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. | Biology, Biochemistry, Cellular Processes | Biochemistry & Molecular Biology, Biological Sciences | Analytical Tool | Documentation, Uses, and more |
| attr | ACES FASTER |
Documentation, Uses, and more | ||||
| attrdict3 | ACES FASTER |
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. | Python Library, Dictionary Wrapper | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| augustus | ACES Bridges-2 FASTER |
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. | Gene Prediction, Eukaryotes, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| autoconf | ACES DeltaAI FASTER KyRIC Stampede3 |
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. | Build Automation, Software Configuration, Makefiles | General, Engineering & Technology | Build Tools | Documentation, Uses, and more |
| autoconf-archive | KyRIC | 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 |
General | Service | Documentation, Uses, and more | |
| autodock | Anvil | 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. | Computational Chemistry, Molecular Docking, Virtual Screening | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| autodock-gpu | FASTER | 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. | Molecular Modeling, Molecular Docking, Biomolecular Interactions, Gpu Acceleration | Bioinformatics, Biological Sciences | Simulation Software | Documentation, Uses, and more |
| autodock-vina | FASTER | AutoDock Vina is an open-source program for doing molecular docking. AutoDock Vina is one of the docking engines of the AutoDock Suite. | Biology | Application | Documentation, Uses, and more | |
| automake | ACES DeltaAI FASTER KyRIC Stampede3 |
Automake is a build automation tool that automatically generates makefiles for software compilation. | Build Automation, Software Development, Compilers | General, Engineering & Technology | Compiler | Documentation, Uses, and more |
| autotools | ACES FASTER Stampede3 |
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. | Programming, Software Development, Build Automation | Software Engineering, Systems & Development, Computer & Information Sciences | Build Automation | Documentation, Uses, and more |
| awkward | FASTER | Documentation, Uses, and more | ||||
| aws-cli | Delta | 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. | Aws, Command Line Interface, Cloud Management | General, Computer & Information Sciences, Engineering & Technology | Command Line Tool | Documentation, Uses, and more |
| aws-cli tool | Anvil | Documentation, Uses, and more | ||||
| awscli | ACES FASTER |
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. | Cloud Computing, Command Line Interface, Aws Services | General, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| axl | FASTER | 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. | Computational Software, Python Library, Materials Science, Software Collaboration | Other Natural Sciences, Physical Sciences | Framework | Documentation, Uses, and more |
| bali-phy | FASTER | 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. | Bayesian Inference, Phylogenetics, Evolutionary Biology, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bamkit | FASTER | 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. | Bioinformatics, Hpc Tools | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| bamtools | ACES Anvil Bridges-2 Delta FASTER |
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. | Bioinformatics, Bam Files, Sequence Alignment, Toolkit | Biology, Biological Sciences | Toolkit | Documentation, Uses, and more |
| bandage | FASTER | Documentation, Uses, and more | ||||
| banner | Delta | 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. | Administrative Software, Higher Education, Student Information System, Academic Records, Financial Aid Management, Human Resources Management | General, Social Sciences | Commercial | Documentation, Uses, and more |
| bar | Stampede3 | Documentation, Uses, and more | ||||
| bat | Bridges-2 | BAT (Bioinformatics Analysis Tool) is a bioinformatics software suite designed for the analysis of biological sequence data. | Bioinformatics, Computational Biology | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| bazel | ACES Bridges-2 FASTER |
Bazel is a build tool that helps to build and test software of any size, quickly and reliably. | Build Tool, Software Testing, Dependency Management, Resource Management | General, Engineering & Technology | Build & Testing Tools | Documentation, Uses, and more |
| bazelisk | ACES FASTER |
Documentation, Uses, and more | ||||
| bbmap | ACES Bridges-2 FASTER |
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. | Bioinformatics, DNA Sequencing, Sequence Alignment | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcbio-gff | FASTER | Documentation, Uses, and more | ||||
| bcftools | ACES Bridges-2 Delta FASTER |
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. | Variant Calling, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bcl2fastq2 | Delta FASTER |
Documentation, Uses, and more | ||||
| bcrypt | ACES FASTER |
Documentation, Uses, and more | ||||
| bdftopcf | DeltaAI | Documentation, Uses, and more | ||||
| beagle | Anvil Delta FASTER |
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. | Phylogenetic Inference, Maximum Likelihood, Molecular Sequence Data, Parallel Processing, Likelihood Calculations | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| beagle-lib | FASTER | 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. | Computational Biology, Phylogenetic Inference, Likelihood Evaluation, Evolutionary Analysis, Bioinformatics | Biology | Library | Documentation, Uses, and more |
| beast | FASTER | 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. | Bioinformatics, Computational Biology, Phylogenetics, Molecular Evolution, Bayesian Analysis | Systems Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| beast2 | Anvil | 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. | Phylogenetics, Evolutionary Analysis, Molecular Sequences, Bayesian Inference | Ecology, Biological Sciences | Tool | Documentation, Uses, and more |
| beautifulsoup | ACES FASTER |
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/ |
General | Library | Documentation, Uses, and more | |
| bedops | Bridges-2 FASTER |
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. | Genomic Data Analysis, Bioinformatics, Computational Biology, Genomics, Data Analysis | Bioinformatics, Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| bedtools | ACES Bridges-2 FASTER |
Bedtools is a software suite for the comparison, manipulation, and annotation of genomic features in multiple formats. | Bioinformatics, Genomics, Data Analysis, Tool | Biology, Biological Sciences | Application | Documentation, Uses, and more |
| bedtools2 | Delta | 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. | Genomic Data Analysis, Bed Files, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| benchmark | ACES | Documentation, Uses, and more | ||||
| berkeley-db | Anvil DeltaAI KyRIC |
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/ |
Storage, Hpc Applications | Library | Documentation, Uses, and more | |
| berkeley-upc | FASTER | 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/ |
Hpc Applications, Parallel Computing | Programming Language | Documentation, Uses, and more | |
| bindcraft | FASTER | Documentation, Uses, and more | ||||
| binutils | ACES FASTER |
Binutils is a collection of binary tools, including linker (ld), assembler (as), archiver (ar), and other tools to manipulate object files and executables. | Binary Tools, Linker, Assembler, Object Files | General, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| bio-db-hts | FASTER | 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. | Python Library, High Throughput Sequencing, Biological Sequence Data, Bioinformatics | Bioinformatics, Biological Sciences | Data Analysis | Documentation, Uses, and more |
| bio-easel | FASTER | Documentation, Uses, and more | ||||
| bio-searchio-hmmer | ACES FASTER |
Documentation, Uses, and more | ||||
| bio-table | FASTER | Documentation, Uses, and more | ||||
| bioawk | FASTER | 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. | Bioinformatics, Data Processing, File Formats, Data Analysis | Bioinformatics, Biological Sciences | Scripting Tool | Documentation, Uses, and more |
| biocontainers | Anvil Stampede3 |
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. | Bioinformatics, Containers, Reproducibility, Software Packaging, Workflow Management | Biology, Biological Sciences | Containerization | Documentation, Uses, and more |
| bioformats | Bridges-2 | 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. | Bioinformatics, Imaging, Biological Data, Data Formats | Biology, Biological Sciences | Library | Documentation, Uses, and more |
| biom-format | ACES FASTER |
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. | Biological Data, High-Throughput Technologies, Data Sharing | Bioinformatics, Biological Sciences | Data Management Tool | Documentation, Uses, and more |
| bioperl | ACES FASTER |
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. | Bioinformatics, Computational Biology, Sequence Analysis, Perl | Genetics, Biological Sciences | Library | Documentation, Uses, and more |
| biopython | ACES FASTER |
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. | Biological Computation, Bioinformatics, Computational Biology, Molecular Biology, Structural Bioinformatics | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| bismark | Anvil Bridges-2 FASTER |
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. | Epigenetics, DNA Methylation, Bisulfite Sequencing, Genomics, Bioinformatics | Genomics, Biological Sciences | Alignment & Methylation Analysis | Documentation, Uses, and more |
| bison | ACES DeltaAI FASTER Ookami Stampede3 |
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. | Parser Generator, Programming Language Tool | General, Computer & Information Sciences | Parser Generator | Documentation, Uses, and more |
| blacs | Ookami | 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. | Linear Algebra, High-Performance Computing, Parallel Computing | Mathematics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| blas | Ookami | Documentation, Uses, and more | ||||
| blast | FASTER | 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. | Bioinformatics, Sequence Alignment, Homology Search | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| blast+ | ACES Bridges-2 FASTER Ookami |
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. | Bioinformatics, Computational Biology, Genomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| blast-plus | Anvil | 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 |
Biology | Tool | Documentation, Uses, and more | |
| blat | ACES Bridges-2 FASTER |
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. | Sequence Analysis, DNA Alignment, Genomic Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| blender | ACES Delta FASTER |
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. | 3D Modeling, Computer Graphics, Animation, Simulation, Open-Source | General, Engineering & Technology | Visual Arts Software | Documentation, Uses, and more |
| blis | ACES Anvil FASTER Ookami Stampede3 |
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. | Blas, Linear Algebra, High Performance Computing, Optimization | Mathematics, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| blosc | ACES FASTER |
Documentation, Uses, and more | ||||
| blosc2 | ACES FASTER |
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. | High-Performance Computing, Compression, Data Storage, Optimization | General, Computer & Information Sciences | Compression | Documentation, Uses, and more |
| bmtagger | FASTER | Documentation, Uses, and more | ||||
| bohrium | FASTER | 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. | High-Performance Computing, Array Programming, Python Integration, Gpu Acceleration | Computer Science, Computer & Information Sciences | High-Performance Computing Tool | Documentation, Uses, and more |
| bokeh | ACES FASTER |
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. | Visualization, Interactive Plots, Data Visualization | General, Computer & Information Sciences | Library | Documentation, Uses, and more |
| bonnie++ | Expanse Ookami |
Documentation, Uses, and more | ||||
| bonsai | FASTER | Documentation, Uses, and more | ||||
| boost | ACES Anvil Bridges-2 Delta Expanse FASTER KyRIC Ookami Stampede3 |
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. | C++ Libraries, Programming Support, Efficiency Enhancement | Computer Science, Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| boost.mpi | ACES FASTER |
Boost.MPI is a peer-reviewed, free, open-source, portable, and fully-standard library implementation of the Message Passing Interface (MPI) for C++. | Mpi, Parallel Computing, C++ | Other Computer & Information Sciences, Computer & Information Sciences | Middleware | Documentation, Uses, and more |
| boost.python | ACES FASTER |
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. | C++, Python, Integration, Library | Mathematics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| boto3 | ACES FASTER |
Documentation, Uses, and more | ||||
| botorch | FASTER | 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. | Bayesian Optimization, Pytorch, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Bayesian Optimization Library | Documentation, Uses, and more |
| bottleneck | FASTER | 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. | Numpy, Array Functions, Performance Optimization | Computer Science, Mathematics, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| bowtie | ACES Delta FASTER |
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. | Bioinformatics, Genomics, DNA Sequencing, Sequence Alignment | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| bowtie2 | ACES Anvil Bridges-2 Delta FASTER |
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. | Alignment, Sequencing Reads, DNA Sequences, High-Throughput Sequencing, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Sequence Alignment | Documentation, Uses, and more |
| bpp | FASTER | Documentation, Uses, and more | ||||
| bracken | FASTER | 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. | Metagenomics, Microbiome, Species Abundance Estimation, Bayesian Analysis | Microbial Ecology, Biological Sciences | Tool | Documentation, Uses, and more |
| breakdancer | FASTER | Documentation, Uses, and more | ||||
| brotli | ACES FASTER |
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. | Compression Algorithm, Lossless Compression, Data Compression | General | Tool | Documentation, Uses, and more |
| brotli-python | ACES | 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. | Compression, Data Compression, Brotli, Python Library | Computer Science, Computer & Information Sciences | Compression Library | Documentation, Uses, and more |
| brunsli | ACES FASTER |
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. | Image Compression, Lossless Compression, High-Speed Encoding | General, Computer & Information Sciences | Image Compressor | Documentation, Uses, and more |
| bs-snper | FASTER | Documentation, Uses, and more | ||||
| btllib | ACES FASTER |
Documentation, Uses, and more | ||||
| build | FASTER | 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. | Task Automation, Build Tool, Software Development | General, Engineering & Technology | Task Automation | Documentation, Uses, and more |
| buildenv | FASTER | Documentation, Uses, and more | ||||
| busco | ACES Bridges-2 FASTER |
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. | Genomics, Genome Assembly, Gene Set, Transcriptome, Orthologs | Bioinformatics, Biological Sciences | Tools | Documentation, Uses, and more |
| bwa | ACES Anvil Bridges-2 FASTER |
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. | Sequence Alignment, Bioinformatics, Genomics, Next-Generation Sequencing (Ngs) | Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| bwa-mem2 | FASTER | Documentation, Uses, and more | ||||
| bwidget | ACES FASTER |
Documentation, Uses, and more | ||||
| bx-python | FASTER | Documentation, Uses, and more | ||||
| byacc | Expanse | 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. | Parser Generator, Lalr, Context-Free Grammar | General, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| bzip2 | ACES Anvil DeltaAI Expanse FASTER KyRIC |
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. | File Compression, Data Compression, Utility Software | General, Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| c-ares | ACES FASTER |
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. | Dns, Asynchronous, Networking, Library, C | General, Computer & Information Sciences | Networking | Documentation, Uses, and more |
| cafe5 | FASTER | Documentation, Uses, and more | ||||
| cairo | ACES Anvil Delta DeltaAI FASTER |
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. | Graphics Library, 2D Graphics, Rendering Engine | Graphics, Computer & Information Sciences | Library | Documentation, Uses, and more |
| caliper | Ookami | Documentation, Uses, and more | ||||
| canu | Bridges-2 FASTER |
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. | Genome Assembly, Nanopore Sequencing, Long-Read Sequencing, Bioinformatics | Genomics, Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cap3 | FASTER | Documentation, Uses, and more | ||||
| capnproto | ACES FASTER |
Documentation, Uses, and more | ||||
| capstone | ACES FASTER |
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. | Disassembly, Binary Analysis, Reverse Engineering | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| captum | ACES | 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. | Interpretability, Model Interpretation, Deep Learning, Pytorch | Artificial Intelligence, Machine Learning, Computer & Information Sciences | Model Interpretation | Documentation, Uses, and more |
| cartopy | ACES FASTER |
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. | Geospatial Data Processing, Data Visualization, Python Library, Mapping, Scientific Visualization | Earth & Environmental Sciences, Physical Sciences | Python Library | Documentation, Uses, and more |
| catch | ACES FASTER |
Documentation, Uses, and more | ||||
| catch2 | ACES FASTER Stampede3 |
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. | Testing Framework, C++, Unit Testing | Computer Science, Engineering & Technology | Testing Framework | Documentation, Uses, and more |
| cath-resolve-hits | FASTER | Documentation, Uses, and more | ||||
| cbc | FASTER | Documentation, Uses, and more | ||||
| cblas | FASTER | Documentation, Uses, and more | ||||
| ccache | ACES FASTER |
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. | Compiler Cache, C/C++ Compilation, Build Optimization | General, Engineering & Technology | Compiler Utility | Documentation, Uses, and more |
| ccdb | Delta DeltaAI |
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. | Cell Cycle, Cell Biology, Database | Cell Biology, Biological Sciences | Curated Data Resource | Documentation, Uses, and more |
| cce | Delta DeltaAI |
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. | Compiler, Interpreter, Programming Language, Compiler Construction | Computer Science, Computer & Information Sciences | Compiler/Interpreter | Documentation, Uses, and more |
| cce-mixed | DeltaAI | 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. | Computational Chemistry, Quantum Mechanics, Electronic Structure Calculations | Condensed Matter Physics, Physical Sciences | Electronic Structure Calculation | Documentation, Uses, and more |
| ccl | KyRIC | 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. | Command Line Interface, C++ Library | Documentation, Uses, and more | ||
| cd-hit | ACES FASTER |
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. | Sequence Analysis, Clustering, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| cdat | FASTER | 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. | Climate Data, Weather Data, Data Analysis, Data Visualization | Atmospheric Sciences, Earth & Environmental Sciences | Tool | Documentation, Uses, and more |
| cdbfasta | FASTER | Documentation, Uses, and more | ||||
| cdo | ACES Anvil Delta FASTER Stampede3 |
Climate Data Operators (CDO) is a collection of command-line operators for manipulating and analyzing climate and numerical weather prediction (NWP) model data. | Climate Data, Data Manipulation, Command Line, Data Analysis | Earth & Environmental Sciences | Command Line Tool | Documentation, Uses, and more |
| cdsapi | ACES | 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). | Python Library, Climate Data, Weather Data | Earth & Environmental Sciences | Api | Documentation, Uses, and more |
| cdtools | Stampede3 | Documentation, Uses, and more | ||||
| cellprofiler | FASTER | Documentation, Uses, and more | ||||
| cellranger | FASTER | 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. | Bioinformatics, Single-Cell RNA-Seq, Data Analysis | Biology, Biological Sciences | Documentation, Uses, and more | |
| cellranger-arc | FASTER | 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. | Single-Cell Analysis, Chromatin Accessibility, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| cellranger-atac | FASTER | 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 | Biology | Application | Documentation, Uses, and more | |
| cellsnp-lite | FASTER | 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. | Variant Calling, Single-Cell RNA Sequencing, Genotyping, Haplotype Inference | Cell Biology, Biological Sciences | Variant Calling Tool | Documentation, Uses, and more |
| centier | FASTER | Documentation, Uses, and more | ||||
| cereal | ACES FASTER |
Cereal is a C++11 library for serialization. It is designed to be fast, compact, and have an easy-to-use API. | Serialization, C++, Library | Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| cesm | FASTER | 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. | Climate Modeling, Earth System Modeling, Global Climate Simulations | Earth & Environmental Sciences | Computational Software | Documentation, Uses, and more |
| cesm-deps | ACES FASTER |
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. | Dependencies, Cesm, Earth System Model, Simulation, Software Package | Earth & Environmental Sciences | Libraries & Dependencies | Documentation, Uses, and more |
| cffi | ACES FASTER |
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. | Foreign Function Interface, C Library Integration, Python | Computer & Information Sciences | Interfacing | Documentation, Uses, and more |
| cfitsio | ACES FASTER Stampede3 |
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | Astronomy, Data Processing, File Format, Fits | Astronomy & Planetary Sciences, Physical Sciences | Data Processing | Documentation, Uses, and more |
| cgal | ACES FASTER |
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. | Computational Geometry, Geometric Algorithms, Software Library | Computer Science, Computer & Information Sciences | Algorithm Library | Documentation, Uses, and more |
| cgl | FASTER | Documentation, Uses, and more | ||||
| cgmlstfinder | FASTER | Documentation, Uses, and more | ||||
| cgns | ACES | 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. | Computational Software | Fluid & Plasma Physics, Physical Sciences | File Format | Documentation, Uses, and more |
| chameleon | ACES | 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. | Python Library, Data Visualization, Color Palette, Visualization, Python | Other Computer & Information Sciences | Library | Documentation, Uses, and more |
| chapel | FASTER Ookami |
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. | Parallel Programming, Hpc, High-Performance Computing, Programming Language | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| charliecloud | FASTER Stampede3 |
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. | Containerization, Software Development, Research Tools | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| charmpp | KyRIC | 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. | Documentation, Uses, and more | |||
| 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/ |
Documentation, Uses, and more | |||
| checkm | ACES Bridges-2 FASTER |
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. | Microbial Genomics, Genome Quality Assessment, Phylogenetic Analysis, Bioinformatics | Ecology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| checkm-database | ACES FASTER |
Documentation, Uses, and more | ||||
| chemprop | ACES | 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. | Chemoinformatics, Molecular Property Prediction, Deep Learning | Chemical Sciences | Bioinformatics | Documentation, Uses, and more |
| chez-scheme | Ookami | Documentation, Uses, and more | ||||
| chimera | FASTER | Documentation, Uses, and more | ||||
| chimerax | ACES FASTER |
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. | Molecular Visualization, Structural Biology, Computational Chemistry | Bioinformatics, Biological Sciences | Analysis & Visualization Tool | Documentation, Uses, and more |
| chimes | FASTER | Documentation, Uses, and more | ||||
| cimfomfa | ACES FASTER |
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. | Documentation, Uses, and more | |||
| circos | Bridges-2 FASTER |
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. | Data Visualization, Genomics, Biological Sciences, Circular Layout | Bioinformatics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| cistem | ACES FASTER |
CISTEM is a computational framework designed for the prediction of dual phase RNA secondary structures. | Computational Framework, RNA Secondary Structures Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ckdmip | ACES | CKDmip is a software for computing cosmic microwave background (CMB) radiation temperature anisotropies and polarization spectra using the Cosmic Microwave Background (CMB) perturbation code. | Cosmic Microwave Background, Cmb Radiation, Temperature Anisotropies, Polarization Spectra | Astronomy & Planetary Sciences, Physical Sciences | Hpc Tool | Documentation, Uses, and more |
| clang | ACES FASTER |
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. | Compiler, Software Development, Programming Languages | Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| clang-aomp | FASTER | 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. | Compiler, Openmp, Gpu Acceleration | Engineering & Technology | Compiler | Documentation, Uses, and more |
| clapack | FASTER | Documentation, Uses, and more | ||||
| clarabel.rs | FASTER | Documentation, Uses, and more | ||||
| clck | KyRIC | Documentation, Uses, and more | ||||
| clhep | ACES FASTER |
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. | C++ Library, High Energy Physics, Hep Applications | Physics, Physical Sciences | Computational Tool | Documentation, Uses, and more |
| climetlab | ACES | 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. | Python Library, Climate Data, Data Visualization | Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| clip | ACES | 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. | Machine Learning, Deep Learning, Image-Text Representation, Pretraining | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning | Documentation, Uses, and more |
| clp | FASTER | 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. | Linear Programming, Optimization, Large-Scale Problems, Open-Source | Operations Research, Industrial Engineering, Engineering & Technology | Solver | Documentation, Uses, and more |
| clustal-omega | FASTER | Documentation, Uses, and more | ||||
| clustalw2 | FASTER | ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. | Bioinformatics, Computational Biology, Sequence Analysis | Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| cluster-tools | Expanse Ookami |
Documentation, Uses, and more | ||||
| cluster-tools-dell | Expanse | Documentation, Uses, and more | ||||
| cm-image | Expanse Ookami |
Documentation, Uses, and more | ||||
| cm-pmix3 | Expanse Ookami |
cm-pmix3 is a lightweight, high-performance library that provides process management and control functions for large-scale computing environments. | Process Management, High-Performance Computing, Job Scheduling | Other Computer & Information Sciences, Engineering & Technology | System & Process Management | Documentation, Uses, and more |
| cm-scale | Expanse Ookami |
Documentation, Uses, and more | ||||
| cm-setup | Expanse Ookami |
Documentation, Uses, and more | ||||
| cmake | ACES Anvil Delta DeltaAI Expanse FASTER KyRIC Ookami Stampede3 |
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. | Build System, Cross-Platform, Software Development | Software Engineering, Systems & Development, Engineering & Technology | Developer Tools | Documentation, Uses, and more |
| cmd | Expanse Ookami |
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. | Command Line, Python Module | Computer & Information Sciences | Framework | Documentation, Uses, and more |
| cmjob | Expanse Ookami |
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. | Hpc, Computational Materials Science, Python Library | Documentation, Uses, and more | ||
| cms3 | FASTER | Documentation, Uses, and more | ||||
| cmseq | FASTER | Documentation, Uses, and more | ||||
| cmsh | Expanse Ookami |
Documentation, Uses, and more | ||||
| cnvnator | FASTER | 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. | Cnv Detection, Whole-Genome Sequencing, Genotyping, Structural Variations | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| cobaya | FASTER | 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. | Bayesian Analysis, Physical Models, Cosmological Models | Astronomy & Planetary Sciences, Physical Sciences | Analysis | Documentation, Uses, and more |
| code-server | FASTER | 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. | Remote Development, Visual Studio Code, Browser-Based Coding, Collaboration, Coding Environment | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| codingquarry | FASTER | Documentation, Uses, and more | ||||
| cogsoft | FASTER | Documentation, Uses, and more | ||||
| coinutils | FASTER | 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. | Optimization, Operations Research, Mathematical Programming | Applied Mathematics, Mathematics | Optimization Software | Documentation, Uses, and more |
| colabfold | ACES FASTER |
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. | Protein Structure Prediction, Deep Learning, Biophysical Modeling | Bioinformatics, Biological Sciences | Protein Structure Prediction Tool | Documentation, Uses, and more |
| colorize | ACES | Documentation, Uses, and more | ||||
| colossalai | ACES FASTER |
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. | Deep Learning Framework, Large-Scale Training, Model Serving | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Open Source | Documentation, Uses, and more |
| compiler | KyRIC | 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, Software Development, Programming | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| compiler-rt | KyRIC | 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. | Runtime Library, Compiler Support, Low-Level Support, Language Features | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| compiler-rt32 | KyRIC | 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. | Compiler, Runtime Library, 32-Bit Architecture | Computer Science, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| compiler32 | KyRIC | 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. | Compiler, Software Development, Programming | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| compleasm | FASTER | Documentation, Uses, and more | ||||
| compress-raw-zlib | FASTER | 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. | Compression, Decompression, Raw Zlib, Library | Computer & Information Sciences | Compression & Decompression | Documentation, Uses, and more |
| comsol | Bridges-2 FASTER |
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. | Simulation, Modeling, Physics, Engineering, Optimization | Engineering & Technology | Simulation Software | Documentation, Uses, and more |
| conan | FASTER | Documentation, Uses, and more | ||||
| concoct | FASTER | 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. | Metagenomics, Bioinformatics, Genomics | Environmental Biology, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| conda | Anvil | Conda is an open source package management system and environment management system for installing multiple versions of software packages and their dependencies and switching easily between them. It works on Linux, OS X and Windows, and was created for Python programs but can package and distribute any software. Description Source: https://github.com/conda-forge/conda-feedstock/blob/main/recipe/meta.yaml | Documentation, Uses, and more | |||
| conda-env | Delta | 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. | Package Management, Environment Management | Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| configurable-http-proxy | ACES FASTER |
Documentation, Uses, and more | ||||
| cooler | FASTER | 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. | Computational Software, Hi-C Data Analysis, Chromatin Interaction Data Analysis | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| coordgenlibs | ACES FASTER |
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. | Computational Chemistry, 3D Coordinate Generation, Small Molecules | Chemical Sciences | Chemical Informatics | Documentation, Uses, and more |
| coreutils | FASTER | Documentation, Uses, and more | ||||
| coverm | FASTER | COVERM is a software tool for the analysis of metagenomic data, particularly for evaluating the coverage and abundance of genes or sequences within metagenomes. | Metagenomics, Bioinformatics, Genomics | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| cp2k | ACES Anvil Bridges-2 FASTER Ookami Stampede3 |
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. | Computational Chemistry, Quantum Mechanics, Molecular Dynamics | Physical Sciences | Molecular Simulation | Documentation, Uses, and more |
| cpe | Delta DeltaAI Ookami |
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. | Software Identification, Cybersecurity, Information Exchange | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| cpe-cuda | Delta DeltaAI |
Documentation, Uses, and more | ||||
| cpe-nosve | Ookami | 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. | Computational Software, Network Analysis, Data Validation, Structure Elucidation | Computer & Information Sciences | Documentation, Uses, and more | |
| cpio | ACES FASTER |
Documentation, Uses, and more | ||||
| cppunit | ACES FASTER |
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. | Unit Testing, C++ | Computer & Information Sciences | Library | Documentation, Uses, and more |
| cppy | ACES FASTER |
C++ embedded Python library to seamlessly interact with C++ and Python code within the same application. | C++, Python, Embedded Python, Interoperability | Computer & Information Sciences | Integration Tool | Documentation, Uses, and more |
| cppzmq | FASTER | Documentation, Uses, and more | ||||
| cpu | Expanse | 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. | Hardware, Computing, Technology | Computer & Information Sciences | Component | Documentation, Uses, and more |
| cray | Ookami | 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. | Supercomputing, High-Performance Computing, Scientific Computing | Computer & Information Sciences | Hpc Tool | Documentation, Uses, and more |
| craype | Delta DeltaAI |
Documentation, Uses, and more | ||||
| craype-accel | Delta DeltaAI |
Documentation, Uses, and more | ||||
| craype-accel-ncsa | Delta | Documentation, Uses, and more | ||||
| craype-x86 | Delta DeltaAI |
Documentation, Uses, and more | ||||
| craypkg-gen | Delta DeltaAI |
Documentation, Uses, and more | ||||
| crb-blast | ACES | Documentation, Uses, and more | ||||
| cromwell | FASTER | Documentation, Uses, and more | ||||
| cryosparc | ACES | CryoSPARC is a comprehensive software platform for cryo-EM data processing that enables high-resolution structure determination of biological macromolecules. | Cryo-Em, Biological Macromolecules, Structural Biology, Data Processing | Biophysics, Biological Sciences | Cryo-Em Software | Documentation, Uses, and more |
| cryptography | ACES FASTER |
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. | Security, Privacy, Encryption, Decryption | Computer & Information Sciences | Software | Documentation, Uses, and more |
| cryptsetup | KyRIC | 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. | Disk Encryption, Data Security, Cryptography, Linux | Computer & Information Sciences | System Software | Documentation, Uses, and more |
| csblast | FASTER | Documentation, Uses, and more | ||||
| ctffind | FASTER | Documentation, Uses, and more | ||||
| cti | Delta DeltaAI |
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. | Threat Intelligence, Data Parsing, Open Source | Computer & Information Sciences | Threat Intelligence | Documentation, Uses, and more |
| cubegui | ACES | Cubegui is a graphical user interface (GUI) software designed for visualizing and analyzing volumetric data in computational chemistry and materials science. | Gui Software, Volumetric Data Visualization, Computational Chemistry, Materials Science | Chemical Sciences, Natural Sciences | Graphical User Interface (Gui) | Documentation, Uses, and more |
| cubelib | ACES | cubelib is a C++ library for parallel reduction operations on multi-dimensional arrays using CUDA. | Software Library, C++, Cuda, Parallel Computing, Multi-Dimensional Arrays | Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cubewriter | ACES | Cubewriter is a software tool that enables researchers to organize, write, and format scientific papers efficiently. | Scientific Writing, Document Formatting, Research Collaboration, References Management | Other Natural Sciences | Productivity Tool | Documentation, Uses, and more |
| cuda | ACES Anvil Bridges-2 Delta DeltaAI FASTER |
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. | Parallel Computing, Gpu Programming, High Performance Computing, Software Development | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| cuda-compat | Delta DeltaAI |
Documentation, Uses, and more | ||||
| cuda-python | ACES | Documentation, Uses, and more | ||||
| cuda-quantum | Anvil | 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. | Quantum Computing, Cuda-Accelerated, Quantum Simulator, Nvidia Gpu, High-Performance Computing | Computer Science, Computer & Information Sciences | Quantum Computing Simulator | Documentation, Uses, and more |
| cuda-samples | ACES FASTER |
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. | Cuda, Gpu Programming, Code Samples, Nvidia | Computer & Information Sciences | Code Sample Repository | Documentation, Uses, and more |
| cuda10.2/blas | Expanse | Documentation, Uses, and more | ||||
| cuda10.2/fft | Expanse | Documentation, Uses, and more | ||||
| cuda10.2/nsight | Expanse | Documentation, Uses, and more | ||||
| cuda10.2/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda10.2/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/blas | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/fft | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/nsight | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda11.7/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/blas | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/fft | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/nsight | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/profiler | Expanse | Documentation, Uses, and more | ||||
| cuda12.2/toolkit | Expanse | Documentation, Uses, and more | ||||
| cuda_python | ACES FASTER |
Documentation, Uses, and more | ||||
| cudacore | ACES FASTER |
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. | Computational Software, Cuda, Gpu Computing, Scientific Computing, Engineering Applications | Other Engineering & Technologies, Engineering & Technology | High-Performance Computing Tool | Documentation, Uses, and more |
| cudatoolkit | DeltaAI | Documentation, Uses, and more | ||||
| cudf | ACES FASTER |
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. | Dataframe, Gpu Acceleration, Data Manipulation | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Library | Documentation, Uses, and more |
| cudnn | ACES Anvil Bridges-2 Delta DeltaAI FASTER |
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. | Deep Learning, Artificial Intelligence, Machine Learning, Gpu Acceleration, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Accelerator | Documentation, Uses, and more |
| cue-login-env | Anvil Delta Expanse |
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. | Python Library, User-Specific Environment, Shared Servers, Computing Clusters | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| cufflinks | Anvil | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. | RNA-Seq, Transcriptomics, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| cunit | ACES FASTER |
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. | Unit Testing, C Programming, Development Tools | Computer & Information Sciences | Testing Framework | Documentation, Uses, and more |
| cupy | ACES FASTER |
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. | Python Library, Gpu Computing, Numpy Replacement | Computer & Information Sciences | Gpu Computing | Documentation, Uses, and more |
| cuquantum-appliance | Anvil | Documentation, Uses, and more | ||||
| curl | ACES Anvil DeltaAI Expanse FASTER KyRIC Ookami |
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. | Networking, Data Transfer, Command-Line, Scripting | Computer & Information Sciences, Other Computer & Information Sciences | Networking Tool | Documentation, Uses, and more |
| cusparselt | ACES FASTER |
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. | Sparse Matrix Operations, Gpu Acceleration, Linear Algebra, Cuda Programming | Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cusz | FASTER | CUSZ is a fast and memory-efficient software tool for clustering and annotating large single-cell RNA-seq datasets. | Single-Cell RNA-Seq, Clustering, Annotation | Cell Biology, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| cutadapt | ACES Bridges-2 FASTER |
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. | Bioinformatics, Ngs, Sequence Analysis, Genomics | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| cutensor | ACES Delta FASTER |
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. | Cuda, Gpu Acceleration, Tensor Operations, Parallel Computing | Applied Computer Science, Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| cutlass | ACES FASTER |
Documentation, Uses, and more | ||||
| cvxopt | FASTER | Documentation, Uses, and more | ||||
| cvxpy | FASTER | Documentation, Uses, and more | ||||
| cxxopts | Stampede3 | A lightweight C++ library for parsing command line arguments, inspired by Python's argparse library. | C++, Command Line Arguments, Parsing, Library | Computer & Information Sciences | Documentation, Uses, and more | |
| cython | ACES FASTER |
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. | Programming Language, C Extensions, Python, Cython | Computer & Information Sciences | Language Compiler | Documentation, Uses, and more |
| cython-blis | ACES | Cython wrapper around BLIS linear algebra library for Python. | Cython, Blis, Linear Algebra, Python | Computer & Information Sciences | Library | Documentation, Uses, and more |
| cytoolz | FASTER | 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. | Python Library, Functional Programming, Utility Functions | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| dace | ACES FASTER |
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. | Data Assimilation, Python Toolkit, Observational Data Integration | Computer & Information Sciences | Documentation, Uses, and more | |
| dagmc | FASTER | Documentation, Uses, and more | ||||
| dal | KyRIC | DAL is a library for collision avoidance in robotics applications. | Robotics, Collision Avoidance | Engineering & Technology | Collision Avoidance Software | Documentation, Uses, and more |
| dalton | FASTER | 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. | Quantum Chemistry, Molecular Properties, Ab Initio Calculations | Physical Chemistry, Chemical Sciences | Simulation | Documentation, Uses, and more |
| dask | ACES FASTER |
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. | Parallel Computing, Scalable Computing, Analytics, Data Science | Computer & Information Sciences | Library | Documentation, Uses, and more |
| dask-labextension | ACES | Documentation, Uses, and more | ||||
| datamash | FASTER | Documentation, Uses, and more | ||||
| datasets | FASTER | 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. | Data, Research, Analysis, Processing, Sharing | Documentation, Uses, and more | ||
| dataspaces | ACES | Documentation, Uses, and more | ||||
| db | ACES FASTER |
db is a simple and minimalistic database library for Python, designed to provide a lightweight interface for basic database operations. | Database, Python Library | Computer & Information Sciences, Computer Science | Library | Documentation, Uses, and more |
| db_file | ACES FASTER |
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. | Database Management, Data Manipulation, Querying, Data Extraction | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| dbcsr | ACES FASTER |
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. | Hpc, Sparse Matrices, Parallel Computing | Other Natural Sciences | Library | Documentation, Uses, and more |
| dbd-mysql | FASTER | 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. | Database, Mysql | Computer & Information Sciences | Software Library | Documentation, Uses, and more |
| dbus | ACES FASTER |
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. | Message Bus System, Interprocess Communication, Process Lifecycle Management | Computer & Information Sciences | Middleware | Documentation, Uses, and more |
| dbus-glib | ACES FASTER |
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. | D-Bus, Inter-Process Communication, Glib | Computer & Information Sciences | Api | Documentation, Uses, and more |
| dcmtk | ACES FASTER |
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. | Dicom, Medical Imaging, Healthcare, Image Processing | Medical & Health Sciences | Data Processing & Analysis | Documentation, Uses, and more |
| ddt | Bridges-2 Stampede3 |
DDT is a powerful, flexible, scalable, and easy-to-use debugging and performance analysis tool for parallel and serial codes. | Debugging Tool, Performance Analysis, Parallel Computing, Serial Computing | Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| dealii | Bridges-2 Stampede3 |
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 |
Library | Documentation, Uses, and more | ||
| debugger | KyRIC | 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. | Debugging, Software Development | Engineering & Technology | Debugger | Documentation, Uses, and more |
| decona | FASTER | Decona is a Conda package management tool that simplifies the installation and management of software packages, dependencies, and environments through the Conda package manager. | Conda, Package Management, Software Installation, Dependency Management | Other Computer & Information Sciences | Conda Package Manager | Documentation, Uses, and more |
| deep_reference_parser | FASTER | Documentation, Uses, and more | ||||
| deepdiff | ACES FASTER |
DeepDiff is a Python library for deep (nested) comparisons of objects. | Python Library, Data Comparison, Object Comparison | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| deeptools | FASTER | 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. | Bioinformatics, Hpc Tools, Computational Software | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| default-environment | Expanse Ookami |
Documentation, Uses, and more | ||||
| default-s11 | Delta | Default-S11 is a high-performance computational software designed for bioinformatics analysis and molecular dynamics simulations. | Computational Software, Bioinformatics, Molecular Dynamics, Sequence Analysis, Protein Structure Prediction | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| defaultmodules | Expanse | Documentation, Uses, and more | ||||
| delly | FASTER | Delly is a structural variant discovery tool that integrates multiple SV detection methods to accurately identify deletions, inversions, duplications, and translocations. | Structural Variant Discovery, Sv Detection, Genomics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| deltalake | ACES FASTER |
Documentation, Uses, and more | ||||
| dendropy | ACES FASTER |
DendroPy is a flexible and modular phylogenetic computing library in Python, offering reading, writing, simulation, and manipulation of phylogenetic trees and associated data. | Phylogenetics, Computational Biology, Python Library, Bioinformatics, Phylogenetic Trees | Biological Sciences | Computational | Documentation, Uses, and more |
| desalt | FASTER | Documentation, Uses, and more | ||||
| desmond | ACES Bridges-2 FASTER |
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. | Molecular Dynamics, Biological Systems, Drug Discovery, Protein Folding | Biochemistry & Molecular Biology, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| dev-utilities | KyRIC | 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. | Development, Utilities | Computer & Information Sciences, Other Computer & Information Sciences | Tools | Documentation, Uses, and more |
| devito | FASTER | 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. | Finite Difference Compiler, Pde Solver, Computational Science | Numerical Analysis, Applied Mathematics | Compiler | Documentation, Uses, and more |
| dft-d3 | FASTER | 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. | Computational Chemistry, Density Functional Theory, Quantum Mechanics | Physical Sciences, Chemical Sciences | Library | Documentation, Uses, and more |
| dftb+ | FASTER | Documentation, Uses, and more | ||||
| dftbplus | FASTER | DFTB+ is an implementation of the Density Functional based Tight Binding (DFTB) method, containing many extensions to the original method. | Documentation, Uses, and more | |||
| dftd3-lib | FASTER | Documentation, Uses, and more | ||||
| dftd4 | FASTER | Documentation, Uses, and more | ||||
| dials | FASTER | Documentation, Uses, and more | ||||
| diamond | ACES FASTER |
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. | Sequence Alignment, Ngs Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| diffutils | KyRIC | 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. | Text Comparison, File Difference, Text Analysis, Version Control | Engineering & Technology | Text Processing | Documentation, Uses, and more |
| dill | ACES FASTER |
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. | Serialization, Python, Datastructures, Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| dimemas | KyRIC | 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. | Performance Prediction, Parallel Applications, Simulation, Large-Scale Systems | Engineering & Technology | Performance Prediction Tool | Documentation, Uses, and more |
| distangsd | FASTER | Documentation, Uses, and more | ||||
| dlib | Delta FASTER |
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. | Machine Learning, Computer Vision, Object Detection, Facial Recognition, Pose Estimation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| dlpack | FASTER | Documentation, Uses, and more | ||||
| dm-haiku | FASTER | Documentation, Uses, and more | ||||
| dm-reverb | FASTER | 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. | Python Library, Data Loading, Data Storage, Machine Learning, Deep Learning | Computer Science | Python Library | Documentation, Uses, and more |
| dm-tree | ACES FASTER |
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. | Python Library, Hierarchical Data, Tree Structures, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| dmfold | FASTER | Documentation, Uses, and more | ||||
| dmlc-core | FASTER | Documentation, Uses, and more | ||||
| dnnl | KyRIC | 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. | Deep Learning, Neural Networks, Machine Learning, Performance Optimization | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| dnnl-cpu-gomp | KyRIC | 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. | Deep Learning, Neural Networks, Openmp, Cpu Computing | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| dnnl-cpu-iomp | KyRIC | dnnl-cpu-iomp is an optimization library for deep neural network computations on CPU using Intel OpenMP (iomp) for improved performance. | Deep Learning, Optimization, Cpu Acceleration | Computer & Information Sciences | Documentation, Uses, and more | |
| dnnl-cpu-tbb | KyRIC | Documentation, Uses, and more | ||||
| docker | Expanse | 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. | Containerization, Deployment, Scalability, Isolation | Computer & Information Sciences | Virtualization | Documentation, Uses, and more |
| dorado | ACES Bridges-2 FASTER |
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. | Performance Evaluation, Benchmarking, Hpc, Supercomputing | Biology, Engineering & Technology | Tool | Documentation, Uses, and more |
| dos2unix | Delta | dos2unix is a command-line utility that converts text files with DOS or Windows line endings (CRLF) to Unix line endings (LF) format. | Text Conversion, Line Endings, Command-Line Utility | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| dot | Expanse Ookami |
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. | Graph Visualization, Open Source, Graph Layout | Computer & Information Sciences | Graph Visualization Software | Documentation, Uses, and more |
| double-conversion | ACES FASTER |
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. | Conversion, Performance, Precision | Computer & Information Sciences | Library | Documentation, Uses, and more |
| doxygen | ACES Expanse FASTER Ookami |
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. | Documentation Generator, Software Development, Programming | Software Engineering, Systems & Development | Tool | Documentation, Uses, and more |
| dpct | KyRIC | 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. | Cuda Programming, Gpu Computing, Parallel Programming | Computer & Information Sciences | Development Compiler | Documentation, Uses, and more |
| dpl | KyRIC | dpl is a software for performing direct programming language analysis. | Programming Language Analysis, Syntax Analysis, Language Structure Analysis | Documentation, Uses, and more | ||
| draco | ACES FASTER |
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. | Compression, 3D Graphics, Geometric Data, Mesh, Point Cloud | Computer & Information Sciences | Library | Documentation, Uses, and more |
| drep | ACES FASTER |
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. | Microbiome, Genome Analysis, Bioinformatics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| drop-seq | FASTER | 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. | Single-Cell RNA Sequencing, Gene Expression Analysis, Microfluidics, Cellular Heterogeneity, Transcriptomics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| ds9 | FASTER | Documentation, Uses, and more | ||||
| dsmml | Delta DeltaAI |
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. | Deep Learning, Molecular Machine Learning, Computational Chemistry, Drug Discovery | Chemical Sciences, Other Chemical Sciences | Deep Learning Library | Documentation, Uses, and more |
| dsuite | FASTER | 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. | Python Library, Data Analysis, Data Visualization | Biostatistics, Statistics & Probability | Python Library | Documentation, Uses, and more |
| dtcmp | FASTER | Documentation, Uses, and more | ||||
| dualsphysics | FASTER | 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. | Computational Fluid Dynamics, Fluid Dynamics, Open-Source Software, Parallel Computing, Sph Method | Fluid Dynamics, Physical Sciences | Computational | Documentation, Uses, and more |
| duckdb | Anvil | Documentation, Uses, and more | ||||
| duplex-tools | FASTER | Documentation, Uses, and more | ||||
| dyninst | Delta DeltaAI |
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. | Binary Instrumentation, Code Analysis, Runtime Monitoring | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| e3nn | FASTER | Documentation, Uses, and more | ||||
| easybuild | ACES FASTER KyRIC |
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. | Software Building, High-Performance Computing, Automation | Engineering & Technology | Build Automation | Documentation, Uses, and more |
| easybuild-aces | ACES | 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. | Software Development, Tools, Packages | Computer & Information Sciences | Tools | Documentation, Uses, and more |
| easybuild-aces-myeb | ACES | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# |
Documentation, Uses, and more | |||
| easybuild-aces-scratch | ACES | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# |
Documentation, Uses, and more | |||
| easybuild-aces-tmp | ACES | 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. | Software Build, Installation Framework, Hpc Systems, Temporary Directory Management | Infrastructure & Instrumentation, Engineering & Technology | Tool | Documentation, Uses, and more |
| easybuild-faster | FASTER | 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. | Hpc, Software Build Optimization, High-Performance Computing | Computer & Information Sciences | Software Framework | Documentation, Uses, and more |
| easybuild-faster-myeb | FASTER | Documentation, Uses, and more | ||||
| easybuild-faster-scratch | FASTER | Documentation, Uses, and more | ||||
| easybuild-faster-tmp | FASTER | Documentation, Uses, and more | ||||
| ecbuild | ACES FASTER |
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. | Build System Generator, Earth System Model, Cmake-Based, Esm Project, Model Coupling, Parallel Execution | Earth & Environmental Sciences | Build System Generator | Documentation, Uses, and more |
| eccodes | ACES FASTER |
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. | Grib Data, Meteorology, Oceanography, Climatology | Atmospheric Sciences, Earth & Environmental Sciences | Data Encoding/Decoding | Documentation, Uses, and more |
| edem | FASTER | Documentation, Uses, and more | ||||
| edirect | FASTER | Documentation, Uses, and more | ||||
| edlib | FASTER | 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. | Sequence Alignment, Edit Distance, Pairwise Alignment | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| ednaflow | FASTER | Documentation, Uses, and more | ||||
| edta | FASTER | 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. | Transcriptome Assembly, RNA-Seq, Gene Annotation | Biological Sciences | Tool | Documentation, Uses, and more |
| egapx | FASTER | Documentation, Uses, and more | ||||
| eggnog-mapper | ACES FASTER |
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. | Functional Annotation, Orthology, Gene Function Prediction | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| eigen | ACES Anvil Delta FASTER Stampede3 |
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | Linear Algebra, Numerical Computation, C++ Library | Computer & Information Sciences | Linear Algebra Library | Documentation, Uses, and more |
| einops | ACES FASTER |
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. | Python Library, Tensor Manipulation, Deep Learning Frameworks | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| elfutils | ACES DeltaAI FASTER |
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. | Binary Tool, Elf Files, Debugging, Programming | Documentation, Uses, and more | ||
| elpa | ACES FASTER Ookami |
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. | Linear Algebra, Eigenvalue Problems, High-Performance Computing, Scalable Algorithms | Computer & Information Sciences | Library | Documentation, Uses, and more |
| elsi | ACES FASTER |
Documentation, Uses, and more | ||||
| emacs | ACES Anvil DeltaAI FASTER |
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. | Text Editor, Customizable, Extensible, Self-Documenting | Computer & Information Sciences | Text Editor | Documentation, Uses, and more |
| eman2 | FASTER | Documentation, Uses, and more | ||||
| emboss | Expanse FASTER |
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. | Bioinformatics, Computational Biology, Sequence Analysis, Biological Data | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| emcee | FASTER | Documentation, Uses, and more | ||||
| emirge | FASTER | Documentation, Uses, and more | ||||
| enchant-2 | ACES FASTER |
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. | Spellchecking, Library, Cross-Platform, Spellchecking Routines | Computer & Information Sciences | Spellchecking | Documentation, Uses, and more |
| energyplus | FASTER | 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. | Energy Simulation, Building Performance, Environmental Control, Parametric Analysis, Building Energy Consumption | Environmental Engineering, Engineering & Technology | Simulation Software | Documentation, Uses, and more |
| 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. | Documentation, Uses, and more | |||
| esm | FASTER | 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. | Earth System Modeling, Climate Simulation, Environmental Processes, Earth System Interactions | Earth & Environmental Sciences | Simulation Tool | Documentation, Uses, and more |
| esmf | ACES FASTER |
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. | Earth System Modeling, Climate Modeling, Weather Modeling, Model Coupling, Earth Science | Earth & Environmental Sciences, Physical Sciences | Computational Software | Documentation, Uses, and more |
| ete | FASTER | Documentation, Uses, and more | ||||
| eviann | FASTER | Documentation, Uses, and more | ||||
| evidencemodeler | FASTER | EvidenceModeler (EM) is a flexible and customizable pipeline for generating gene structure annotations by integrating evidence from various prediction programs and transcriptomic data. | Gene Prediction, Annotation, Bioinformatics, Transcriptomics, Genomics | Bioinformatics, Biological Sciences | Pipeline | Documentation, Uses, and more |
| exiv2 | ACES FASTER |
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. | Metadata Management, Image Processing, Command-Line Utility | Computer & Information Sciences | Metadata Management | Documentation, Uses, and more |
| exllsm-circuit-reconstruction | FASTER | Documentation, Uses, and more | ||||
| exo | FASTER | Documentation, Uses, and more | ||||
| exonerate | FASTER | 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. | Sequence Alignment, Homology Search, Bioinformatics, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| expat | ACES Anvil DeltaAI FASTER KyRIC |
Expat is an XML parser library written in C. It is a fast and lightweight library that is designed for high-performance applications. | Xml Parser, Library | Computer & Information Sciences | Xml Parser | Documentation, Uses, and more |
| expect | ACES FASTER |
Documentation, Uses, and more | ||||
| expecttest | ACES FASTER |
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. | Testing Tool, Automation, Scripting, Software Development | Automation Tool | Documentation, Uses, and more | |
| extrae | KyRIC | 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. | Performance Analysis, Trace Data, Parallel Applications, Distributed Applications | Computer & Information Sciences, Software Engineering, Systems & Development, Engineering & Technology, Training, Infrastructure & Instrumentation | Tool | Documentation, Uses, and more |
| eztrace | ACES | 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. | Performance Analysis, Function Call Tracing, Profiling, Monitoring | Computer & Information Sciences | Library Tool | Documentation, Uses, and more |
| falcon | FASTER | Documentation, Uses, and more | ||||
| fasta | ACES FASTER |
Documentation, Uses, and more | ||||
| fastahack | ACES FASTER |
Documentation, Uses, and more | ||||
| fastai | ACES | 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. | Deep Learning, Neural Networks, Machine Learning, Pytorch | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| fastaindex | FASTER | Documentation, Uses, and more | ||||
| fastani | ACES Bridges-2 FASTER |
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. | Bioinformatics, Genome Comparison, Bacterial Genomes | Biology, Biological Sciences | Genome Analysis Tool | Documentation, Uses, and more |
| fastcore | FASTER | 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. | Python Library, Utility Library, Data Manipulation, Functional Programming | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| fastfilters | FASTER | Documentation, Uses, and more | ||||
| fastme | FASTER | Documentation, Uses, and more | ||||
| fastp | Delta FASTER |
fastp is a tool designed for pre-processing high throughput sequencing data faster and more efficiently. | Bioinformatics, Sequencing, Data Processing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| fastq-tools | Bridges-2 | 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. | Bioinformatics, Ngs, Genome Sequencing, Sequence Analysis | Bioinformatics, Biological Sciences | Data Processing Tool | Documentation, Uses, and more |
| fastqc | ACES Anvil Bridges-2 Delta FASTER |
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. | Quality Control, High Throughput Sequencing, Sequence Analysis, Bioinformatics | Biology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| fastsimcoal2 | FASTER | Documentation, Uses, and more | ||||
| fastsimcoal26 | FASTER | Documentation, Uses, and more | ||||
| fasttree | ACES Anvil FASTER |
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. | Phylogenetics, Bioinformatics, Computational Biology, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| fastx-toolkit | Anvil Bridges-2 FASTER |
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. | Bioinformatics, Ngs Data Processing, Sequence Analysis, Fastq Manipulation | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| fdasrsf | FASTER | A python package for functional data analysis using the square root slope framework and curves using the square root velocity framework which performs pair-wise and group-wise alignment as well as modeling using functional component analysis and regression. Description Source: https://github.com/conda-forge/fdasrsf-feedstock/blob/main/recipe/meta.yaml | Documentation, Uses, and more | |||
| femzip-l | FASTER | 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. | Compression, Finite Element Models, Engineering, Computational Sciences | Engineering & Technology | Tool | Documentation, Uses, and more |
| fermi-lite | ACES FASTER |
Documentation, Uses, and more | ||||
| fetk | ACES | Documentation, Uses, and more | ||||
| ffmpeg | ACES Anvil Bridges-2 Delta FASTER Ookami Stampede3 |
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. | Media Processing, Multimedia, Video, Audio | Engineering & Technology | Tool | Documentation, Uses, and more |
| ffnvcodec | ACES FASTER |
ffnvcodec is a codec library provided by NVIDIA for efficient video encoding and decoding using the NVIDIA GPU hardware acceleration. | Codec, Video Processing, Gpu Acceleration | Computer & Information Sciences | Library | Documentation, Uses, and more |
| fftw | ACES Anvil Bridges-2 Delta DeltaAI FASTER KyRIC |
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. | Signal Processing, Data Compression, Partial Differential Equations | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| fftw.mpi | ACES FASTER |
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. | Computational Software, Hpc Tools | Mathematics | Tool | Documentation, Uses, and more |
| fftw2 | Stampede3 | Documentation, Uses, and more | ||||
| fftw3 | Ookami Stampede3 |
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. | Fft, Fourier Transform, Open-Source, Computational Physics | Condensed Matter Physics, Physical Sciences | Numerical Library | Documentation, Uses, and more |
| figtree | FASTER | Documentation, Uses, and more | ||||
| fiji | ACES FASTER |
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. | Image Processing, Scientific Research, Image Analysis | Other Natural Sciences | Analysis Tool | Documentation, Uses, and more |
| file | ACES FASTER |
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. | File Management, Command-Line Utility | Command Line Tool | Documentation, Uses, and more | |
| filevercmp | ACES FASTER |
Documentation, Uses, and more | ||||
| filtlong | Bridges-2 FASTER |
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. | Bioinformatics, Long Read Sequencing, Sequence Data Processing | Biological Sciences | Data Filtering Tool | Documentation, Uses, and more |
| findbin | FASTER | Documentation, Uses, and more | ||||
| findutils | DeltaAI | Documentation, Uses, and more | ||||
| finestructure | FASTER | Documentation, Uses, and more | ||||
| fiona | ACES FASTER |
Fiona is a Python library for reading and writing geospatial vector data formats. | Python Library, Geospatial Data, Gis, Vector Data | Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| firefox | ACES FASTER |
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. | Web Browser, Internet, Privacy, Open-Source, Cross-Platform | Computer & Information Sciences | Web Browser | Documentation, Uses, and more |
| firestarter | FASTER | 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. | Firewall, Network Security, Linux | Computer & Information Sciences | Security Tool | Documentation, Uses, and more |
| fixchr | FASTER | Documentation, Uses, and more | ||||
| flac | ACES FASTER |
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. | Audio Codec, Open-Source, Lossless Compression | Other Computer & Information Sciences | Compression Tool | Documentation, Uses, and more |
| flake8 | FASTER | Documentation, Uses, and more | ||||
| flash | ACES Bridges-2 FASTER |
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. | Computational Software, Numerical Simulation, Fluid Dynamics, Electromagnetics, Structural Analysis | Physical Sciences | Computational Physics | Documentation, Uses, and more |
| flash-attention | FASTER | Documentation, Uses, and more | ||||
| flask | ACES FASTER |
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. | Web Development, Python, Framework, Web Applications | Computer & Information Sciences | Open Source | Documentation, Uses, and more |
| flatbuffers | ACES FASTER |
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. | Serialization, Data Storage, Communication, Efficiency, Cross-Platform | Computer & Information Sciences | Library | Documentation, Uses, and more |
| flatbuffers-python | ACES FASTER |
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/ |
Library | Documentation, Uses, and more | ||
| flex | ACES DeltaAI FASTER Ookami |
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. | Lexical Analyzer, Text Processing, Pattern Matching, Scanner Generator | Documentation, Uses, and more | ||
| flexiblas | ACES Delta FASTER |
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. | Blas Library, Scientific Computing, Linear Algebra | Other Mathematics | Library | Documentation, Uses, and more |
| flit | ACES FASTER |
Flit is a simple tool for building and distributing Python packages. | Python Packaging, Package Management | Computer & Information Sciences | Building & Distribution Tool | Documentation, Uses, and more |
| flow-3d | FASTER | Documentation, Uses, and more | ||||
| fltk | ACES FASTER |
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. | Gui Toolkit, Cross-Platform Development, C++ Library | Engineering & Technology | Development Tool | Documentation, Uses, and more |
| flye | FASTER | 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. | Genome Assembly, Long-Read Sequencing, Nanopore Sequencing | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| fms2 | Ookami | 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. | Compiler, Software, Translation | Other Computer & Information Sciences | Source-To-Source Compiler | Documentation, Uses, and more |
| fmt | ACES FASTER |
Documentation, Uses, and more | ||||
| foldseek | FASTER | 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. | RNA Secondary Structure Prediction, Deep Learning Models, Python Package | Biological Sciences | Library | Documentation, Uses, and more |
| font-util | Anvil DeltaAI |
Documentation, Uses, and more | ||||
| fontconfig | ACES Anvil DeltaAI FASTER |
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. | Fontconfig, Font Management, Font Configuration, Linux, Unix-Like Systems | Engineering & Technology | System Tool | Documentation, Uses, and more |
| fontsproto | DeltaAI | Documentation, Uses, and more | ||||
| fonttools | FASTER | Documentation, Uses, and more | ||||
| foss | ACES FASTER |
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. | Free Software, Open Source Software, Software Development | Other Computer & Information Sciences | Software Library | Documentation, Uses, and more |
| fosscuda | ACES FASTER |
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. | Cuda, Gpu Computing, Parallel Programming, Open-Source | Computer Science, Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| fraggenescan | FASTER | 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. | Gene Prediction, Ngs Data Analysis, Metagenomics, Single-Cell Sequencing | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| freebayes | ACES FASTER |
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. | Genetic Variant Detector, Snp Detection, Indel Detection, Bayesian Algorithm | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| freeglut | ACES FASTER |
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. | Graphics Programming, Opengl, Cross-Platform Development, Free Software | Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| freeimage | FASTER | FreeImage is an open-source graphics library that supports popular image formats and features image loading, saving, conversion, manipulation, and processing capabilities. | Graphics Library, Image Processing, Open-Source | Engineering & Technology | Graphics Library | Documentation, Uses, and more |
| freeipmi | Expanse Ookami |
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. | Bmc, Baseboard Management Controller, Open-Source, Hardware Management, Monitoring | Computer & Information Sciences | Management & Monitoring Tool | Documentation, Uses, and more |
| freesurfer | Expanse FASTER |
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. | Neuroimaging, Mri Analysis, Brain Segmentation, Functional Mri, Image Visualization | Neuroscience, Biological Sciences | Scientific | Documentation, Uses, and more |
| freetype | ACES Anvil DeltaAI FASTER |
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. | Font Engine, Text Rendering, Typography | Computer & Information Sciences | Font Engine | Documentation, Uses, and more |
| freexl | ACES FASTER |
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. | Excel, Spreadsheet, Data Extraction | Computer & Information Sciences | Data Extraction | Documentation, Uses, and more |
| fribidi | ACES DeltaAI FASTER Ookami |
GNU FriBidi is an implementation of the Unicode Bidirectional Algorithm (bidi). It also provides utility functions to help work with bidirectional text. | Unicode, Bidirectional Algorithm | Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| fsa | FASTER | Documentation, Uses, and more | ||||
| fsl | FASTER | 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. | Mri, Imaging, Neuroimaging, Data Analysis, Image Processing | Biological Sciences | Image Processing Software | Documentation, Uses, and more |
| fsom | ACES FASTER |
Documentation, Uses, and more | ||||
| fujitsu | 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. | It Services, Information Technology, Hardware, Software | Computer & Information Sciences | Documentation, Uses, and more | |
| funannotate | Bridges-2 | 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. | Genome Prediction, Genome Annotation, Fungi, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| futhark | FASTER | 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. | Programming Language, Data-Parallel Programming, Gpu Programming, High-Performance Computing | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| g2clib | ACES FASTER |
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. | Geophysics, Meteorology, Data Manipulation, Data Analysis | Earth & Environmental Sciences | Computational Tool | Documentation, Uses, and more |
| g2lib | ACES FASTER |
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. | Computational Geometry, Computer Graphics, Geometric Computing | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| gambit | Ookami | 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. | Game Theory, Computational Analysis, Nash Equilibria | Economics & Business, Social Sciences | Software Package | Documentation, Uses, and more |
| gamess | Bridges-2 Stampede3 |
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. | Quantum Chemistry, Electronic Structure Calculations, Ab Initio Calculations | Physical Sciences, Chemical Sciences | Quantum Chemistry | Documentation, Uses, and more |
| gapcloser | FASTER | Documentation, Uses, and more | ||||
| gappa | FASTER | Documentation, Uses, and more | ||||
| garcon | FASTER | Documentation, Uses, and more | ||||
| gatb-core | ACES | Documentation, Uses, and more | ||||
| gatk | ACES Anvil Bridges-2 FASTER |
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. | Variant Calling, Genotyping, Sequencing Analysis | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| gaussian | Bridges-2 FASTER Stampede3 |
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. | Computational Chemistry, Quantum Chemistry, Molecular Modeling | Chemical Sciences, Natural Sciences | Simulation Software | Documentation, Uses, and more |
| gawk | FASTER KyRIC |
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. | Text Processing, Data Manipulation, Pattern Scanning | Chemistry, Computer & Information Sciences | Text Processing Tool | Documentation, Uses, and more |
| gc | ACES FASTER |
GC is a compiler for the Go programming language. | Compiler, Go, Garbage Collection, Concurrency | Computer Science, Computer & Information Sciences | Programming Language Compiler | Documentation, Uses, and more |
| gcatools | FASTER | 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. | Genomic Data Analysis, Next-Generation Sequencing, Bioinformatics | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| gcc | ACES Anvil Bridges-2 Delta DeltaAI Expanse FASTER KyRIC Ookami |
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. | Compiler, Software Development, Programming | Computer Science | Development Tools | Documentation, Uses, and more |
| gcc compilers | Stampede3 | Documentation, Uses, and more | ||||
| gcc-native | Delta DeltaAI |
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. | Compiler, Gnu, Programming Language | Computer Science, Computer & Information Sciences | Native Compiler | Documentation, Uses, and more |
| gcc-native-mixed | DeltaAI | 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. | Compiler, Mixed-Language Programming, Optimization | Computer Science | Development Tool | Documentation, Uses, and more |
| gcc-runtime | Delta | 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. | Compiler, Runtime, Library | Software Engineering, Systems & Development, Engineering & Technology | Runtime Library | Documentation, Uses, and more |
| gcccore | ACES FASTER |
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. | Compiler, Programming, Software Development | Computer & Information Sciences, Software Engineering, Systems & Development | Core Component | Documentation, Uses, and more |
| gcccuda | ACES FASTER |
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. | Cuda Programming, C Compiler Wrapper, Parallel Computing | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| gcloud | FASTER | Documentation, Uses, and more | ||||
| gconf | ACES FASTER |
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. | Configuration Management, Settings, Preferences, Desktop Environment | Computer & Information Sciences | Configuration Management System | Documentation, Uses, and more |
| gcta | FASTER | Documentation, Uses, and more | ||||
| gd | FASTER | Documentation, Uses, and more | ||||
| gdal | ACES Anvil DeltaAI FASTER Stampede3 |
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. | Geospatial Data, Raster Data, Vector Data, Data Formats, Geospatial Analysis | Earth & Environmental Sciences, Engineering & Technology | Library | Documentation, Uses, and more |
| gdb | ACES Anvil Delta DeltaAI Expanse FASTER Ookami |
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. | Debugger, Programming, Software Development | Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| gdb4hpc | Delta DeltaAI |
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. | Debugging, Hpc, Parallel Programming, Performance Analysis | Computer Science, Engineering & Technology | Plugin | Documentation, Uses, and more |
| gdbm | Anvil DeltaAI FASTER KyRIC |
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. | Database Management, Key-Value Store, Persistent Storage, Api | Computer & Information Sciences | Library | Documentation, Uses, and more |
| gdc-client | KyRIC | Documentation, Uses, and more | ||||
| gdk-pixbuf | ACES FASTER |
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. | Image Processing, Graphics, Library | Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| gdown | ACES FASTER |
Documentation, Uses, and more | ||||
| gdrcopy | ACES Delta FASTER |
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. | Gpu Memory Copy, Cuda Acceleration, Asynchronous Memory Copies | Computer Science, Computer & Information Sciences | Memory Management | Documentation, Uses, and more |
| geant4 | ACES FASTER |
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. | Software, Physics, Simulation, Particle Transport | Particle Physics, Physical Sciences | Toolkit | Documentation, Uses, and more |
| geant4-data | ACES | Datasets for Geant4. | Documentation, Uses, and more | |||
| gem | FASTER | Documentation, Uses, and more | ||||
| gemma | FASTER | 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. | Genome-Wide Association Analysis, Genetic Analysis, Mixed Model Framework | Biological Sciences | Genetic Analysis | Documentation, Uses, and more |
| genemark-es | Bridges-2 | 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. | Gene Prediction, Bioinformatics, Eukaryotic Genomes, Hidden Markov Model | Biological Sciences | Gene Prediction Software | Documentation, Uses, and more |
| genemark-et | FASTER | Documentation, Uses, and more | ||||
| 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. | Documentation, Uses, and more | |||
| genericrepeatfinder | FASTER | Documentation, Uses, and more | ||||
| genomealignmenttools | FASTER | Documentation, Uses, and more | ||||
| genomepy | ACES | 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. | Genomics, Bioinformatics, Python, Reference Genomes, Sequence Analysis | Genomics, Biological Sciences | Python Library | Documentation, Uses, and more |
| genomethreader | FASTER | Documentation, Uses, and more | ||||
| genometools | FASTER | Documentation, Uses, and more | ||||
| gent | Bridges-2 | 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. | DNA Comparison, Structural Variants, Genomics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| geocube | ACES FASTER |
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. | Geospatial Data, 3D Visualization, Python Library | Earth & Environmental Sciences, Physical Sciences | Python Library | Documentation, Uses, and more |
| geopandas | ACES FASTER |
Geopandas is an open-source python library for working with geospatial data, enabling users to easily manipulate and analyze geospatial datasets. | Geospatial Data, Python Library, Geospatial Analysis | Earth & Environmental Sciences | Data Analysis | Documentation, Uses, and more |
| geos | ACES Anvil DeltaAI FASTER Ookami |
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. | Geometry Engine, Spatial Data Processing, Gis, Open-Source | Other Computer & Information Sciences, Computer & Information Sciences | Geospatial Software | Documentation, Uses, and more |
| getdist | FASTER | 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. | Mcmc Analysis, Parameter Estimation, Posterior Plots, Cosmology | Astronomy & Planetary Sciences, Physical Sciences | Python Library | Documentation, Uses, and more |
| gethost | Ookami | 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. | Networking, Command-Line, System Administration | Computer & Information Sciences | Networking Tool | Documentation, Uses, and more |
| gettext | ACES Anvil Bridges-2 DeltaAI FASTER KyRIC |
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. | Internationalization, Localization, Software Development | Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| gfatools | FASTER | 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. | Genomics, Genome Variation Graphs, Sequence Alignment, Variation Analysis | Biological Sciences | Tool | Documentation, Uses, and more |
| gfbf | ACES FASTER |
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. | Compiler, Boolean Functions, Logic Synthesis, Verification, Optimization | Computer Science, Computer & Information Sciences | Compilation Tool | Documentation, Uses, and more |
| gffcompare | Delta FASTER |
gffcompare is a tool for evaluating the accuracy of RNA-Seq transcript assemblers and for annotating genomic features. | RNA-Seq, Transcript Assembly, Genome Annotation | Biological Sciences | Computational Tool | Documentation, Uses, and more |
| gffread | FASTER | 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. | Gff3, Fasta, Sequence Processing | Biological Sciences | Tool | Documentation, Uses, and more |
| gffutils | FASTER | 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. | Genomic Data, Bioinformatics, Python Library, File Parsing, Data Manipulation | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gflags | FASTER | Documentation, Uses, and more | ||||
| gh | Delta Expanse FASTER |
Github CLI. Description Source: https://github.com/conda-forge/gh-feedstock/blob/main/recipe/meta.yaml | Documentation, Uses, and more | |||
| ghostscript | ACES Anvil FASTER |
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. | Document-Processing, File-Conversion, Print-Management | Computer & Information Sciences, Engineering & Technology | Software Development | Documentation, Uses, and more |
| giflib | ACES FASTER |
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. | Library, Image Processing, Gif Images | Package | Documentation, Uses, and more | |
| git | ACES Delta FASTER KyRIC Ookami |
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. | Version Control, Software Development, Source Code Management | Computer & Information Sciences, Software Engineering, Systems & Development | Development Tools | Documentation, Uses, and more |
| git-lfs | ACES Delta DeltaAI FASTER |
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. | Version Control, File Storage, Git Extension | Engineering & Technology | Development Tool | Documentation, Uses, and more |
| gitpython | ACES FASTER |
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. | Version Control, Source Code Management, Python Library | Computer Science | Development | Documentation, Uses, and more |
| gklib | ACES Stampede3 |
gklib is a C++ library for geometric kernels that provides efficient and accurate geometric algorithms for computational geometry and related fields. | Geometric Kernels, Computational Geometry, Algorithms | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| gl2ps | ACES FASTER |
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. | Opengl, Postscript, Printing, Graphics, Vector Graphics | Library | Documentation, Uses, and more | |
| glances | Ookami | A cross-platform curses-based monitoring tool Description Source: https://github.com/conda-forge/glances-feedstock/blob/main/recipe/meta.yaml | Documentation, Uses, and more | |||
| glew | ACES FASTER |
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. | Opengl, Extension Loader, C/C++ Library | Computer Science | Tool | Documentation, Uses, and more |
| glfw | ACES FASTER |
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. | Graphics, Opengl, Cross-Platform, Window Management, Input Handling | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| glib | ACES Anvil DeltaAI FASTER |
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. | Utility Library, C Programming, Data Structures, Memory Management, Thread Support | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| glib-networking | ACES FASTER |
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. | Glib, Network, Linux, Library | Computer & Information Sciences | Documentation, Uses, and more | |
| glibc | FASTER Ookami |
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. | C Library, Operating System, System Programming | Computer & Information Sciences | Library | Documentation, Uses, and more |
| glibmm | FASTER | Documentation, Uses, and more | ||||
| glimmerhmm | FASTER | 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. | Gene Prediction, Microbial Genomes, Hidden Markov Models, Bioinformatics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| glm | ACES Delta FASTER |
glm is a Python library for Generalized Linear Models (GLM) with support for exponential family distributions. | Python Library | Mathematics | Library | Documentation, Uses, and more |
| globalarrays | ACES FASTER Ookami |
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | Documentation, Uses, and more | |||
| globus-cli | ACES FASTER |
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. | Command-Line Interface, File Transfer Service, Data Management, Data Transfer | Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| glog | FASTER | Documentation, Uses, and more | ||||
| glpk | ACES FASTER |
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. | Linear Programming, Optimization, Open-Source | Applied Mathematics, Mathematics | Mathematical Optimization | Documentation, Uses, and more |
| gmap-gsnap | ACES FASTER |
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. | RNA-Seq, Bioinformatics, Mapping, Alignment | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| gmp | ACES Anvil DeltaAI Expanse FASTER KyRIC Stampede3 |
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. | Computational Software, Library, Mathematics, Software Development | Pure Mathematics, Mathematics | Library | Documentation, Uses, and more |
| gmpich | FASTER | Documentation, Uses, and more | ||||
| gmpy2 | ACES FASTER |
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. | Python Library, Arbitrary-Precision Arithmetic, Gmp Library, Mpfr Library | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| gmt | Anvil | 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. | Mapping, Geographic Data, Cartesian Data, Illustration, Postscript, Map Projections | Earth & Environmental Sciences | Command Line Tool | Documentation, Uses, and more |
| gnu autotools | KyRIC | Documentation, Uses, and more | ||||
| gnu compiler collection | KyRIC | Documentation, Uses, and more | ||||
| 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/ |
Documentation, Uses, and more | |||
| gnuconfig | DeltaAI | Documentation, Uses, and more | ||||
| gnupg-bundle | FASTER | Documentation, Uses, and more | ||||
| gnuplot | ACES Anvil Delta DeltaAI Expanse FASTER Ookami |
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. | Graphing, Visualization, Data Analysis | Physical Sciences | Plotting & Data Visualization | Documentation, Uses, and more |
| gnutls | ACES DeltaAI FASTER |
GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols, providing various cryptographic algorithms. | Security, Encryption, Networking | Computer & Information Sciences | Library | Documentation, Uses, and more |
| go | ACES Expanse FASTER KyRIC Ookami |
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/ |
Documentation, Uses, and more | |||
| go-bootstrap | KyRIC | 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. | Go, Template, Project Structure, Best Practices | Engineering & Technology | Template Project | Documentation, Uses, and more |
| gobff | FASTER | 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. | Protein Structure Prediction, Fragment Assembly, Monte Carlo Simulations | Bioinformatics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| gobject-introspection | ACES DeltaAI FASTER |
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. | Middleware, Language Bindings, Automation, Compatibility | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| gomkl | ACES FASTER |
Documentation, Uses, and more | ||||
| gompi | ACES FASTER |
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. | Hpc, Parallel Computing, Mpi, Distributed Computing | Engineering & Technology | Documentation, Uses, and more | |
| gompic | ACES FASTER |
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. | Simulation, Granular Materials, Collective Dynamics, Soft Matter | Other Physical Sciences, Physical Sciences | Research | Documentation, Uses, and more |
| googletest | ACES FASTER |
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. | Unit Testing, C++ Testing, Testing Library, Software Testing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| gpaw | ACES FASTER |
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. | Dft, Electronic Structure, Quantum Mechanics | Condensed Matter Physics, Physical Sciences | Simulation | Documentation, Uses, and more |
| gpaw-setups | ACES FASTER |
Documentation, Uses, and more | ||||
| gperf | ACES DeltaAI FASTER Ookami |
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. | Perfect Hash Function, Hash Table, Optimization, Gnu | Computer Science, Computer & Information Sciences | Compiler/Generator | Documentation, Uses, and more |
| gperftools | ACES FASTER Ookami |
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. | Performance Analysis, Profiling, C/C++ | Engineering & Technology | Tool | Documentation, Uses, and more |
| gpflow | ACES FASTER |
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. | Machine Learning, Probabilistic Programming, Gaussian Processes | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Documentation, Uses, and more | |
| gpgme | ACES | Documentation, Uses, and more | ||||
| gpu | Expanse | 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. | Software, Computational Software, Hpc Tools, Gpu, Parallel Processing | Engineering & Technology, Computer & Information Sciences | Hardware | Documentation, Uses, and more |
| gpustat | ACES FASTER |
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. | Gpu Monitoring, System Administration, Python Library, Command-Line Tool | Computer Science, Engineering & Technology | Library | Documentation, Uses, and more |
| gpy | FASTER | GPy is a Gaussian process framework in Python for implementing Gaussian processes. It offers tools for Gaussian process regression, classification, optimization, and more. | Machine Learning, Data Analysis, Python, Gaussian Processes | Computer & Information Sciences | Data Analysis | Documentation, Uses, and more |
| gpytorch | ACES FASTER |
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. | Machine Learning, Gaussian Processes, Deep Learning | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| graalvm | FASTER | 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. | Software Development, Runtime Environment, Polyglot Programming, Just-In-Time Compilation, Native Image Generation | Computer & Information Sciences | Compiler/Runtime | Documentation, Uses, and more |
| gradle | FASTER | 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. | Build Automation, Dependency Management, Java, Groovy | Computer & Information Sciences | Tools | Documentation, Uses, and more |
| grads | Anvil | 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. | Data Visualization, Meteorology, Climatology, Earth Science, Data Analysis | Earth & Environmental Sciences | Desktop Application | Documentation, Uses, and more |
| graphblas | ACES | GraphBLAS is a collection of high-performance linear algebraic operations specifically designed for sparse graphs and matrices. | Graph, Linear Algebra, Sparse Matrices | Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphene | ACES FASTER |
Graphene is a Python library for building GraphQL APIs fast and easily. | Python Library, Graphql | Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphicsmagick | ACES FASTER |
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. | Image Processing, Graphics, Media Editing, Command-Line Tools | Other Computer & Information Sciences | Image Processing Software | Documentation, Uses, and more |
| graphite2 | ACES FASTER |
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. | Font Rendering, Typography, Smart Fonts | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| graphviz | ACES FASTER |
Graphviz is open source graph visualization software. It is used for creating structured diagrams such as flowcharts, network diagrams, and more. | Graph Visualization, Diagramming, Open Source Software | Computer & Information Sciences | Data Visualization | Documentation, Uses, and more |
| graphviz-python | ACES FASTER |
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. | Graph Visualization, Python Library, Network Analysis | Computer & Information Sciences | Visualization Tool | Documentation, Uses, and more |
| grass | ACES FASTER |
Documentation, Uses, and more | ||||
| great_tables | ACES | Documentation, Uses, and more | ||||
| greenlet | ACES FASTER |
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. | Python Library, Concurrency, Coroutines | Computer & Information Sciences | Programming | Documentation, Uses, and more |
| groff | ACES FASTER |
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. | Typesetting, Text Formatting, Unix Utilities | Computer & Information Sciences | Typesetting System | Documentation, Uses, and more |
| gromacs | ACES Anvil Bridges-2 Delta FASTER KyRIC Ookami Stampede3 |
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. | Molecular Dynamics, Simulation, High Performance Computing, Biomolecular Systems | Chemistry, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| grpc | FASTER | 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. | Rpc, Distributed Systems, Communication | Computer & Information Sciences, Software Engineering, Systems & Development | Library/Framework | Documentation, Uses, and more |
| grpcio | ACES FASTER |
Documentation, Uses, and more | ||||
| gsd-vmd | FASTER | 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. | Molecular Dynamics, Simulation Analysis, Trajectory Visualization | Other Natural Sciences | Documentation, Uses, and more | |
| gsl | ACES Anvil Delta DeltaAI FASTER Stampede3 |
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. | Numerical Library, Mathematical Functions, C Programming, C++ Programming | Mathematics, Other Mathematics | Library | Documentation, Uses, and more |
| gslib | ACES FASTER |
gslib is an open-source and free collection of Fortran 77 subroutines for geostatistical applications. | Geostatistics, Fortran 77, Spatial Data, Variogram Modeling, Kriging | Geoscience, Earth & Environmental Sciences | Geospatial Analysis Tool | Documentation, Uses, and more |
| gst-plugins-bad | ACES FASTER |
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. | Multimedia, Plugin, Gstreamer | Computer & Information Sciences | Plugin | Documentation, Uses, and more |
| gst-plugins-base | ACES FASTER |
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. | Audio Processing, Video Processing, Multimedia Framework | Computer Science, Computer & Information Sciences | Plugin | Documentation, Uses, and more |
| gstreamer | ACES Anvil FASTER |
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. | Multimedia, Framework, Media Processing, Audio, Video | Computer & Information Sciences | Framework | Documentation, Uses, and more |
| gtdb-tk | FASTER | Documentation, Uses, and more | ||||
| gthumb | Delta | gthumb is an image viewer and browser for the GNOME desktop environment. It also includes features for organizing and managing images. | Image Viewer, Image Browser, Image Management | Other Computer & Information Sciences | Desktop Application | Documentation, Uses, and more |
| gtk+ | FASTER | 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. | Gui Toolkit, Graphical User Interface, Desktop Application Development | Computer & Information Sciences | Toolkit | Documentation, Uses, and more |
| gtk2 | ACES FASTER |
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. | Gui, Widget Toolkit, Cross-Platform | Biology, Computer & Information Sciences | Gui Toolkit | Documentation, Uses, and more |
| gtk3 | ACES FASTER |
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. | Gui Toolkit, Desktop Application Development, Cross-Platform Development, User Interface Design | Biology, Computer & Information Sciences | Development Toolkit | Documentation, Uses, and more |
| gtk4 | ACES FASTER |
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. | Gui Toolkit, Cross-Platform Development, User Interface Design | Biology, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| gts | ACES FASTER |
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. | Computational Geometry, Surface Properties, Mesh Generation | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| guile | ACES FASTER |
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. | Programming Language, Scripting Language, Embeddable, Customizable | Computer & Information Sciences | Interpreter | Documentation, Uses, and more |
| guppy | Bridges-2 | 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. | Bioinformatics, Sequencing, Nanopore Sequencing, Genomics, DNA Sequencing | Genomics, Biological Sciences | Basecaller | Documentation, Uses, and more |
| guppy-gpu | Bridges-2 | 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. | Basecaller, Oxford Nanopore, Sequencing, Gpu Acceleration | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| gurobi | Anvil Bridges-2 Delta FASTER |
Gurobi Optimization is a high-performance mathematical programming solver for linear programming (LP), mixed-integer programming (MIP), and other related optimization problems. | Optimization, Mathematical Programming, Linear Programming, Mixed-Integer Programming | Mathematics | Solver | Documentation, Uses, and more |
| gurobi-dev | Delta | Documentation, Uses, and more | ||||
| gymnasium | ACES FASTER |
Gymnasium is a Python library which provides tools and utilities for creating and manipulating complex mathematical expressions and equations. | Python Library, Mathematical Expressions, Equation Manipulation | Computer Science, Mathematics | Programming Library | Documentation, Uses, and more |
| gzip | ACES DeltaAI FASTER |
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. | File Compression, Data Storage, Data Transfer | Engineering & Technology | Compression Tool | Documentation, Uses, and more |
| h5py | ACES FASTER |
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. | Python Library, Data Storage, Numerical Data, Data Manipulation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| hadoop | Anvil Delta Expanse FASTER |
Hadoop is an open-source framework used for distributed storage and processing of large sets of data on computer clusters using simple programming models. | Big Data, Data Processing, Distributed Computing | Computer & Information Sciences | Framework | Documentation, Uses, and more |
| haphic | FASTER | Documentation, Uses, and more | ||||
| harfbuzz | ACES DeltaAI FASTER Ookami |
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. | Text Shaping Engine, Unicode Text, Text Layout, Font Features Customization | Computer & Information Sciences | Library | Documentation, Uses, and more |
| harvest-tools | FASTER | Documentation, Uses, and more | ||||
| hashdeep | Bridges-2 | hashdeep is a cross-platform hashing utility that calculates and verifies hash signatures for files and directories. | Hashing, Data Integrity, Security | Computer & Information Sciences | Hashing | Documentation, Uses, and more |
| hatch-jupyter-builder | ACES FASTER |
Documentation, Uses, and more | ||||
| hatchling | ACES FASTER |
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. | Population Dynamics, Ecology, Simulation, Environmental Factors | Environmental Biology, Biological Sciences | Research Tool | Documentation, Uses, and more |
| hdbscan | FASTER | 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. | Clustering Algorithm, Data Mining, Unsupervised Learning, Machine Learning | Computer & Information Sciences | Data Mining Tool | Documentation, Uses, and more |
| hdf | ACES Anvil FASTER |
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. | Data Management, File Format, Data Visualization, Api | Other Computer & Information Sciences | File Format | Documentation, Uses, and more |
| hdf-eos | ACES | 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. | Data Management, Data Processing, Earth Science, Geospatial Data | Earth & Environmental Sciences, Physical Sciences | Library | Documentation, Uses, and more |
| hdf-eos5 | ACES | 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. | Nasa, Earth Observing System, Data Management, Data Analysis, Hdf5 Format | Earth & Environmental Sciences, Natural Sciences | Data Management & Analysis | Documentation, Uses, and more |
| hdf5 | ACES Anvil Bridges-2 Delta DeltaAI Expanse FASTER Ookami Stampede3 |
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. | File Format, Data Management, Data Storage, Data Sharing, High-Performance Computing | Other Computer & Information Sciences | Library/Tool | Documentation, Uses, and more |
| hdf5-parallel | DeltaAI | Documentation, Uses, and more | ||||
| hdf5_18 | Expanse Ookami |
Documentation, Uses, and more | ||||
| healpix | FASTER | Documentation, Uses, and more | ||||
| heffte | ACES | Documentation, Uses, and more | ||||
| helitronscanner | FASTER | Documentation, Uses, and more | ||||
| help2man | ACES FASTER |
help2man is a tool that can generate simple man pages from the '--help' and '--version' output of other commands. | Documentation, Man Pages, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| herro | FASTER | Documentation, Uses, and more | ||||
| hh-suite | ACES FASTER |
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. | Protein Sequence Searching, Profile Hidden Markov Models, Protein Structure Prediction | Biological Sciences | Computational Software | Documentation, Uses, and more |
| hic-pro | FASTER | 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. | Bioinformatics, Genomics, Chromatin Structure, Hi-C Data, Data Visualization, Chromatin Interactions | Genomics, Biological Sciences | Data Analysis | Documentation, Uses, and more |
| hicexplorer | FASTER | 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. | Hi-C Data Analysis, Genome 3D Organization, Genomics | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| hicmatrix | FASTER | Documentation, Uses, and more | ||||
| hifiasm | FASTER | Hifiasm is a fast and scalable haplotype-resolved de novo assembler for PacBio HiFi reads. | Assembler, De Novo Assembly | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| hifiasm-meta | FASTER | Documentation, Uses, and more | ||||
| highfive | Stampede3 | Documentation, Uses, and more | ||||
| highway | ACES FASTER |
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. | Bioinformatics, Computational Biology, Statistical Analysis | Bioinformatics, Biological Sciences | Statistical Tool | Documentation, Uses, and more |
| hipify | ACES | Documentation, Uses, and more | ||||
| hipify-clang | FASTER | 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. | Cuda, Hip, Gpu Computing, Code Translation | Computer & Information Sciences | Code Translation Tool | Documentation, Uses, and more |
| hipsycl | FASTER | hipsycl is a SYCL implementation targeting CPUs, CUDA, and HIP backends for heterogeneous systems, allowing for portable performance across different hardware platforms. | Heterogeneous Computing, Parallel Programming, Hardware Acceleration | Computer Science, Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| hiredis | ACES FASTER |
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. | Redis, Database, C Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| hisat2 | ACES Bridges-2 Delta FASTER |
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. | Alignment, Ngs, Genomics, Transcriptomics | Biology, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| hmmer | ACES Bridges-2 FASTER |
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. | Bioinformatics, Computational Biology, Proteomics, Sequence Analysis | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| hmmer2 | FASTER | Documentation, Uses, and more | ||||
| homer | Bridges-2 | 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. | Bioinformatics, Next-Generation Sequencing, Motif Discovery, Transcription Factor Binding Sites | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| horovod | ACES FASTER |
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. | Deep Learning, Distributed Training, Machine Learning, Gpu Acceleration, High Performance Computing | Computer & Information Sciences | Library/Framework | Documentation, Uses, and more |
| hossedu | FASTER | HOSSedu is an educational software tool designed for teaching and learning in the field of computer science and programming. | Educational Software, Computer Science, Programming | Computer Science, Computer & Information Sciences | Teaching & Learning Tool | Documentation, Uses, and more |
| hpc-x | ACES | 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. | Hpc, High-Performance Computing, Scientific Computing, Parallel Computing | Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| hpctoolkit | Anvil Delta |
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/ |
Documentation, Uses, and more | |||
| hpl | ACES FASTER |
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. | Hpc, Benchmarking, Performance Analysis | Infrastructure & Instrumentation, Engineering & Technology | Benchmarking Tool | Documentation, Uses, and more |
| hprc_utils | ACES FASTER |
hprc_utils is a collection of utility tools for managing and analyzing High Performance Computing (HPC) environments and workflows. | Hpc, High Performance Computing, Utility Tools | Engineering & Technology | Tool | Documentation, Uses, and more |
| htop | Delta DeltaAI FASTER Ookami |
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. | System Monitoring, Process Viewer, Resource Usage | Engineering & Technology | Monitoring Tool | Documentation, Uses, and more |
| htseq | ACES FASTER |
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. | Bioinformatics, RNA-Seq, High-Throughput Sequencing, Gene Expression, Sequence Data | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| htslib | ACES Bridges-2 Delta FASTER |
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. | Bioinformatics, Sequencing Data, File Format Processing, C Library | Genomics, Biological Sciences | Data Processing | Documentation, Uses, and more |
| huggingface_hub | ACES | Documentation, Uses, and more | ||||
| humann | ACES FASTER |
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. | Metagenomics, Microbiome, Pathway Analysis, Bioinformatics | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| hunspell | ACES FASTER |
Hunspell is a spell checker and morphological analyzer software designed for languages with rich morphology and complex word compounding. | Spell Checker, Morphological Analyzer, Language Support | Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| hwloc | ACES Anvil Bridges-2 Expanse FASTER KyRIC Ookami |
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. | Machine Topology, Hardware Architecture, System Software | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| hydra | FASTER | Documentation, Uses, and more | ||||
| hyper-shell | Anvil | hyper-shell is a command-line terminal replacement that aims to enhance the user experience and productivity through various features and customizations. | Terminal Emulator, Productivity Tool, Command-Line Interface | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| hyperopt | ACES FASTER |
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. | Optimization, Machine Learning, Statistics | Computer & Information Sciences | Documentation, Uses, and more | |
| hypershell | Anvil | Documentation, Uses, and more | ||||
| hyphen | FASTER | 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. | Word Hyphenation, Text Formatting, Tex Patterns | Other Mathematics | Utility Tool | Documentation, Uses, and more |
| hyphy | FASTER | 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. | Bioinformatics, Molecular Evolution, Phylogenetics, Epidemiology | Bioinformatics, Biological Sciences | Open-Source Software | Documentation, Uses, and more |
| hypothesis | ACES FASTER |
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. | Python Testing Tool, Property-Based Testing, Automated Test Generation | Computer Science, Computer & Information Sciences | Property-Based Testing Tool | Documentation, Uses, and more |
| hypre | ACES FASTER Ookami Stampede3 |
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. | Preconditioners, Solvers, Linear Systems, Sparse Matrices | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| iaf2 | ACES FASTER |
Documentation, Uses, and more | ||||
| iccifort | FASTER | 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. | Compiler, High-Performance Computing, Optimization | Engineering & Technology | Programming Tool | Documentation, Uses, and more |
| iccifortcuda | FASTER | 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. | Hpc, Compiler, Cuda, Parallel Programming | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| iced | FASTER | Documentation, Uses, and more | ||||
| icon | ACES | Documentation, Uses, and more | ||||
| icu | ACES FASTER |
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. | Unicode Support, Globalization, Localization, Internationalization, Unicode Libraries | Computer & Information Sciences | Libraries | Documentation, Uses, and more |
| icu4c | Delta DeltaAI KyRIC |
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. | Unicode, Globalization, Cross-Platform, Libraries | Computer & Information Sciences | Development | Documentation, Uses, and more |
| idba-ud | FASTER | Documentation, Uses, and more | ||||
| idev | Stampede3 | idev is a compiler wrapper that simplifies the use of Intel's data parallel C++ (DPC++) compiler for offloading computations to GPUs. | Compiler Wrapper, Dpc++ Compiler, Gpu Offloading | Computer Science, Computer & Information Sciences | Tool | Documentation, Uses, and more |
| idl | Expanse Stampede3 |
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. | Software, Data Analysis, Data Visualization, Scientific Research | Physical Sciences | Programming Language | Documentation, Uses, and more |
| igprof | ACES FASTER |
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. | Profiler, Performance Analysis, Code Optimization, Software Development | Engineering & Technology | Tool | Documentation, Uses, and more |
| igraph | FASTER | Documentation, Uses, and more | ||||
| igv | FASTER | 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. | Visualization, Genomics, Sequencing, Data Analysis | Biological Sciences | Genomics Software | Documentation, Uses, and more |
| iimkl | FASTER | Documentation, Uses, and more | ||||
| iimpi | ACES FASTER |
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. | Ion Mobility-Mass Spectrometry, Peak Integration, Data Analysis | Bioinformatics, Biological Sciences | Analytical Tool | Documentation, Uses, and more |
| iimpic | FASTER | 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. | Python Library, Porous Materials, Lattice Boltzmann Method | Physical Sciences | Simulation Software | Documentation, Uses, and more |
| ijulia | ACES | Documentation, Uses, and more | ||||
| imageio | ACES FASTER |
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. | Python Libraries, Image Processing, Data Visualization | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| imagej | ACES FASTER |
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. | Image Processing, Scientific Tool, Java-Based, Open-Source | Documentation, Uses, and more | ||
| imagemagick | ACES Delta FASTER Ookami |
ImageMagick is a free and open-source software suite for creating, editing, composing, or converting bitmap images. | Image Processing, Graphics Editing, Conversion Tool | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| imake | ACES | 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. | Build Automation, Software Development, Build Configuration | Software Engineering, Systems & Development, Engineering & Technology | Automation Tool | Documentation, Uses, and more |
| imath | ACES FASTER |
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. | Mathematics, Computational Software, Simulation, Data Analysis | Mathematics | Mathematical Modeling & Analysis Software | Documentation, Uses, and more |
| imb | KyRIC | IMB stands for In-Memory Database benchmark. It is a benchmarking tool specifically designed to evaluate the performance of in-memory databases. | Benchmarking, In-Memory Databases | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| imbalanced-learn | ACES FASTER |
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. | Imbalanced Datasets, Machine Learning, Classification Tasks, Python Library, Over-Sampling, Under-Sampling, Ensemble Techniques | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| imkl | ACES FASTER |
imkl is a open-source software library for creating and managing knowledge graphs for various applications in artificial intelligence, data science, and information retrieval. | Software Library, Knowledge Graph, Artificial Intelligence, Data Science, Information Retrieval | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Open-Source | Documentation, Uses, and more |
| imkl-fftw | ACES FASTER |
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. | Software Library, Math Library, Mathematical Computation, Fourier Transforms, High-Performance Computing | Mathematics | Mathematical Computation | Documentation, Uses, and more |
| iml | ACES | Interpretable Machine Learning | Machine Learning, Interpretability, Model Explanation | Computer & Information Sciences | R Package | Documentation, Uses, and more |
| impi | ACES Anvil FASTER |
impi is a high-performance message passing library that provides asynchronous messaging and queuing functionalities for parallel computing applications. | Message Passing Library, Parallel Computing, Asynchronous Messaging | Engineering & Technology | Communication Library | Documentation, Uses, and more |
| impute2 | Delta | IMPUTE2 is a tool for imputing ungenotyped markers in large-scale genome-wide association studies. | Genotype Imputation, Genome-Wide Association Studies, Bioinformatics | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| infercnv | FASTER | Documentation, Uses, and more | ||||
| infernal | ACES Bridges-2 FASTER |
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. | RNA Sequence Analysis, Bioinformatics, Sequence Alignment | Documentation, Uses, and more | ||
| init_opencl | KyRIC | init_opencl is a software library that is used to initialize OpenCL platforms and create OpenCL contexts for parallel computing applications. | Software, Compiler, Library, Hpc | Computer & Information Sciences | Software Development | Documentation, Uses, and more |
| inputproto | Delta DeltaAI FASTER |
A package that provides the headers used to compile Xlib clients. | Software Development, Headers, Xlib | Computer & Information Sciences | Library | Documentation, Uses, and more |
| inq | FASTER | 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. | Inventory Management, System Administration | Computer & Information Sciences, Other Computer & Information Sciences | Command-Line Interface | Documentation, Uses, and more |
| inspector | KyRIC | 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. | Monitoring, Security, Network Analysis | Computer Science, Computer & Information Sciences | Security Software | Documentation, Uses, and more |
| intel | ACES Bridges-2 Expanse FASTER Jetstream2 Ookami |
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. | Semiconductor, Technology, Microprocessors | Engineering & Technology | Hardware | Documentation, Uses, and more |
| intel compiler | KyRIC | 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. | Compiler, Optimization, Performance, Debugging | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel oneapi compiler | Stampede3 | Documentation, Uses, and more | ||||
| intel(r) mpi library | Stampede3 | Documentation, Uses, and more | ||||
| intel-advisor | Bridges-2 | Documentation, Uses, and more | ||||
| intel-ccl | Bridges-2 | Documentation, Uses, and more | ||||
| intel-cluster-runtime | Ookami | Documentation, Uses, and more | ||||
| intel-compiler | Bridges-2 | 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. | Compiler, Optimization, Performance, Parallelization | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel-compiler-rt | Bridges-2 | 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. | Compiler, Runtime Library, Performance Optimization | Computer & Information Sciences | Compiler Runtime Library | Documentation, Uses, and more |
| intel-compiler-rt32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-compiler32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-compilers | ACES FASTER |
Intel C, C++ & Fortran compilers (classic and oneAPI) | Documentation, Uses, and more | |||
| intel-dal | Bridges-2 | 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. | Security, Intel Platform, Dynamic Code Loading, Trusted Applications | Documentation, Uses, and more | ||
| intel-debugger | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dev-utilities | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dnnl | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dnnl-cpu-gomp | Bridges-2 | Documentation, Uses, and more | ||||
| intel-dnnl-cpu-iomp | Bridges-2 | 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. | Deep Learning, Cpu Optimization, Neural Networks | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| intel-dnnl-cpu-tbb | Bridges-2 | 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. | Deep Learning, Neural Networks, Cpu Optimization, Threading Building Blocks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning Library | Documentation, Uses, and more |
| intel-dpct | Bridges-2 | 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, Data Migration, Cuda, Dpc++, Heterogeneous Computing | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| intel-dpl | Bridges-2 | 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. | Parallel Programming, High Performance Computing, Intel Architecture | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| intel-icc | Bridges-2 | Documentation, Uses, and more | ||||
| intel-icc32 | Bridges-2 | 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. | Compiler, Software Development, Optimization | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| intel-inspector | Bridges-2 | 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. | Software, Development, Debugging, Memory Management, Multithreading | Engineering & Technology | Memory & Threading Error Checker | Documentation, Uses, and more |
| intel-ipp-ia32 | Bridges-2 | 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. | Software Library, Performance Optimization, Signal Processing, Image Processing, Cryptography | Computer Science, Computer & Information Sciences | Shared Library | Documentation, Uses, and more |
| intel-ipp-intel64 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-ippcp-ia32 | Bridges-2 | 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. | Software Library, Cryptography, Security | Computer & Information Sciences | Program Library | Documentation, Uses, and more |
| intel-ippcp-intel64 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-itac | Bridges-2 | Documentation, Uses, and more | ||||
| intel-mkl | Anvil Bridges-2 |
Intel Math Kernel Library (MKL) contains ScaLAPACK, LAPACK, Sparse Solver, BLAS, Sparse BLAS, CBLAS, GMP, FFTs, DFTs, VSL, VML, and Interval Arithmetic routines. | Documentation, Uses, and more | |||
| intel-mkl32 | Bridges-2 | Documentation, Uses, and more | ||||
| intel-mpi | Anvil Bridges-2 |
Documentation, Uses, and more | ||||
| intel-oclfpga | Bridges-2 | 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. | Development Tools, Accelerating Workloads, Fpga Programming, Hardware Acceleration | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| intel-oneapi | Bridges-2 | Documentation, Uses, and more | ||||
| intel-oneapi-compilers | Delta | Documentation, Uses, and more | ||||
| intel-oneapi-mkl | Delta | Documentation, Uses, and more | ||||
| intel-parallel-studio | Anvil | Documentation, Uses, and more | ||||
| intel-python | FASTER | Documentation, Uses, and more | ||||
| intel-tbb | Bridges-2 Delta |
Documentation, Uses, and more | ||||
| intel-tbb32 | Bridges-2 | 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. | Parallelism, C++, Multi-Core, Library | Computer & Information Sciences, Computer Science, Applied Computer Science | Library | Documentation, Uses, and more |
| intel-vtune | Bridges-2 | Documentation, Uses, and more | ||||
| intel/aikit | ACES | Documentation, Uses, and more | ||||
| intel_ai_toolkit | Delta | Documentation, Uses, and more | ||||
| intel_ipp_ia32 | KyRIC | Documentation, Uses, and more | ||||
| intel_ipp_intel64 | KyRIC | 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. | Software Development, Performance Optimization, Data Processing, Signal Processing, Image Processing, Cryptography | Computer & Information Sciences, Software Engineering, Systems & Development | Commercial | Documentation, Uses, and more |
| intel_ippcp_ia32 | KyRIC | 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. | Cryptographic Library, Performance Optimization, Intel Architecture | Computer & Information Sciences | Compiler/Library | Documentation, Uses, and more |
| intel_ippcp_intel64 | KyRIC | 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. | Cryptography, High-Performance Computing, Intel Processors, Security | Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| intelclusterchecker | ACES | Documentation, Uses, and more | ||||
| intelcuda | FASTER | Documentation, Uses, and more | ||||
| intelmpi | Bridges-2 | 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. | Hpc, Mpi Library, Intel Architecture | Engineering & Technology | Library | Documentation, Uses, and more |
| intelpython | ACES | Documentation, Uses, and more | ||||
| intermol | Bridges-2 | Documentation, Uses, and more | ||||
| interproscan | FASTER | 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. | Bioinformatics, Proteomics, Sequence Analysis, Functional Annotation | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| intervaltree | ACES FASTER |
Documentation, Uses, and more | ||||
| intervaltree-python | FASTER | Documentation, Uses, and more | ||||
| intltool | ACES FASTER |
Intltool is a set of tools to centralize translation of many different file formats using a single language-styled file. | Localization, Translation, Internationalization | Computer & Information Sciences | Localization Tool | Documentation, Uses, and more |
| iomkl | FASTER | 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. | Math Kernel Library, High-Performance Computing, Linear Algebra, Mathematical Operations | Mathematics | Library | Documentation, Uses, and more |
| iompi | FASTER | 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. | Computational Software, Numerical Methods, Partial Differential Equations, Scientific Computing | Applied Mathematics, Physical Sciences | Library | Documentation, Uses, and more |
| ior | Delta | 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. | High-Performance Computing, Parallel Computing, I/O Optimization | Computer Science | Utility Software | Documentation, Uses, and more |
| iozone | Expanse Ookami |
Documentation, Uses, and more | ||||
| iperf3 | Delta DeltaAI |
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. | Network Testing, Bandwidth Measurement, Network Performance | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| ipmitool | Expanse Ookami |
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. | System Management, Hardware Monitoring, Remote Administration, Open Source | Engineering & Technology | Utility | Documentation, Uses, and more |
| ipython | ACES FASTER |
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. | Command Shell, Interactive Computing, Data Visualization, Parallel Computing, Data Analysis | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| iq-tree | FASTER | 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. | Phylogenetics, Bioinformatics, Computational Biology, Phylogenomic Analysis | Systematics & Population Biology, Biological Sciences | Phylogenetic Tree Construction Tool | Documentation, Uses, and more |
| irf | FASTER | Documentation, Uses, and more | ||||
| irkernel | ACES | Documentation, Uses, and more | ||||
| irods-icommands | Bridges-2 | iCommands, the default command line interface to iRODS. | Documentation, Uses, and more | |||
| isa-l | ACES FASTER |
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. | Optimized Functions, Data Movement, Data Protection, Storage Applications | Engineering & Technology | Documentation, Uses, and more | |
| isl | ACES FASTER |
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. | Library, Integer Points, Linear Constraints | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| itac | KyRIC Stampede3 |
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. | Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| itk | ACES FASTER |
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. | Image Processing, Medical Imaging, Scientific Images | Medical & Health Sciences, Engineering & Technology | Image Analysis | Documentation, Uses, and more |
| jackie2 | FASTER | Documentation, Uses, and more | ||||
| jags | FASTER | 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. | Bayesian Statistics, Hierarchical Modeling, Mcmc Simulation | Statistics & Probability, Mathematics | Statistical Modeling | Documentation, Uses, and more |
| jansson | ACES FASTER |
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. | Json, C Library, Data Parsing, Data Manipulation | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| jasper | ACES Delta FASTER |
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. | Image Processing, Open-Source, Jpeg-2000 | Computer Science, Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| java | ACES FASTER |
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. | Programming Language, Computing Platform | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jax | ACES Delta FASTER |
JAX is an open-source software library for high-performance machine learning research, particularly for automatic differentiation, and numerical and scientific computing. | Machine Learning, Numerical Computing, Scientific Computing | Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| 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/ |
Documentation, Uses, and more | |||
| jbrowse | FASTER | Documentation, Uses, and more | ||||
| jdftx | FASTER | 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. | Computational Software, Electronic Structure Calculations, Materials Science | Physical Sciences | Simulation Software | Documentation, Uses, and more |
| jedi | ACES FASTER |
Documentation, Uses, and more | ||||
| jellyfish | ACES FASTER |
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. | K-Mer Counting, DNA Sequences, Sequence Analysis | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| jemalloc | ACES FASTER |
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. | Memory Allocator, Performance Optimization, Multithreading | Computer & Information Sciences | Memory Allocator | Documentation, Uses, and more |
| jmol | ACES FASTER |
Jmol is an open-source Java viewer for chemical structures in 3D with features for visualization, analysis, and manipulation of molecular structures. | Molecular Visualization, Molecular Analysis, Chemistry | Physical Chemistry, Inorganic & Nuclear Chemistry, Chemical Sciences | Modeling & Simulation | Documentation, Uses, and more |
| jq | FASTER | Documentation, Uses, and more | ||||
| json-c | ACES DeltaAI FASTER KyRIC |
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. | C Library, Json Encoding, Json Decoding, Data Manipulation | Computer Science, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| json-fortran | FASTER | Documentation, Uses, and more | ||||
| json-glib | DeltaAI | Documentation, Uses, and more | ||||
| jsonc | Stampede3 | Documentation, Uses, and more | ||||
| jsoncpp | ACES FASTER |
JsonCpp is a C++ library that allows manipulating JSON data structures. It provides features for parsing, generating, and manipulating JSON data in C++ applications. | C++, Json, Library, Data Manipulation | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| judy | ACES FASTER |
Judy is a C library that provides a collection of functions to efficiently manage data arrays to store and retrieve key/value pairs. | C Library, Data Management, Key/Value Pairs | Other Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| juicer | FASTER | Documentation, Uses, and more | ||||
| juicer_tools | FASTER | Documentation, Uses, and more | ||||
| julia | ACES Anvil Bridges-2 Delta FASTER Ookami |
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. | Programming Language, Technical Computing, High-Performance Computing, Scientific Computing, Numerical Analysis | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| julia_tamu | ACES | Documentation, Uses, and more | ||||
| junit | FASTER | 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. | Unit Testing, Java, Testing Framework | Software Engineering, Systems & Development, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| jupyter | Anvil Ookami |
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. | Data Science, Scientific Computing, Machine Learning | Computer & Information Sciences | Web Application | Documentation, Uses, and more |
| jupyter-bundle | ACES FASTER |
Documentation, Uses, and more | ||||
| jupyter-notebook | Ookami | Documentation, Uses, and more | ||||
| jupyter-resource-usage | ACES FASTER |
Documentation, Uses, and more | ||||
| jupyter-server | ACES FASTER |
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. | Interactive Computing, Web-Based Interface, Notebooks | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| jupyter-server-proxy | ACES FASTER |
Documentation, Uses, and more | ||||
| jupyterhub | ACES FASTER |
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. | Data Science, Collaborative Computing, Notebook Environment, Interactive Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Collaborative Tool | Documentation, Uses, and more |
| jupyterlab | ACES FASTER |
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. | Interactive Computing, Data Visualization, Jupyter Notebooks, Web-Based Interface, Code Editing | Computer & Information Sciences | Data Science Tool | Documentation, Uses, and more |
| jupyterlmod | ACES FASTER |
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. | Jupyter Notebook, Environment Modules, Software Environment Management | Other Natural Sciences | Extension | Documentation, Uses, and more |
| jupyternotebook | ACES FASTER |
The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience. | Documentation, Uses, and more | |||
| kahip | ACES FASTER |
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. | Graph Partitioning, High-Performance Computing, Parallel Computing | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| kaiju | FASTER | 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. | Bioinformatics, Computational Biology, Genomics, Sequencing Data | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| kaks_calculator | FASTER | Documentation, Uses, and more | ||||
| kaleido | ACES FASTER |
Documentation, Uses, and more | ||||
| kalign | ACES FASTER |
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. | Bioinformatics, Sequence Alignment, DNA, RNA, Protein, Wu-Manber Algorithm | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kallisto | ACES FASTER |
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. | RNA-Seq, Transcriptomics, Bioinformatics, Gene Expression Analysis, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| kblas-gpu | ACES | 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. | Linear Algebra, Gpu-Accelerated, Hpc, Parallel Computing | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| kbproto | Delta DeltaAI FASTER |
The kbproto package provides the core XKB protocol and extension definitions for usage with X11 protocol libraries. | X11 Protocol, Keyboard Properties | Computer Science, Computer & Information Sciences | Protocol | Documentation, Uses, and more |
| kent_tools | FASTER | Documentation, Uses, and more | ||||
| keras | ACES Anvil FASTER |
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. | Neural Networks, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| kim-api | ACES FASTER |
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. | Computational Software, Hpc Tools | Materials Science, Physical Sciences | Application Programming Interface | Documentation, Uses, and more |
| kineto | ACES FASTER |
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. | Mechanical Engineering, Simulation, Mechanical Systems, Kinematics, Dynamics | Engineering & Technology | Analysis Tool | Documentation, Uses, and more |
| kma | FASTER | KMA (K-mer Matching Alignment) is a tool for mapping sequencing reads to reference sequences. It utilizes k-mer based alignment to efficiently and accurately map reads in both nucleotide and amino acid sequence data. | Sequence Alignment, Read Mapping, Bioinformatics | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| knime | Bridges-2 | KNIME is an open-source data analytics, reporting, and integration platform. It allows users to visually design data flows, execute data processing, data cleansing, analysis, and reporting without needing to write any code. | Data Analytics, Data Integration, Data Visualization | Informatics, Analytics & Information Science, Computer & Information Sciences | Data Analysis Tool | Documentation, Uses, and more |
| knitro | FASTER | Knitro is a proprietary software package for solving large-scale optimization problems. It provides a suite of optimization algorithms designed to handle continuous nonlinear optimization problems efficiently. Knitro is suitable for solving problems with thousands to millions of variables and constraints. | Optimization, Large-Scale, Nonlinear, Modeling | Other Mathematics | Solver | Documentation, Uses, and more |
| kokkos | Delta Ookami Stampede3 |
Kokkos is a programming model for writing performance portable parallel applications in C++. It allows developers to write code once and run efficiently on multiple types of heterogeneous architectures. | Programming Model, Performance Portability, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| korflab-perl_utils | FASTER | Documentation, Uses, and more | ||||
| kraken | FASTER | Documentation, Uses, and more | ||||
| kraken2 | ACES Bridges-2 Delta FASTER |
Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm. Description Source: https://github.com/DerrickWood/kraken2/wiki/About-Kraken-3 |
Documentation, Uses, and more | |||
| krb5 | Anvil | Documentation, Uses, and more | ||||
| krbalancing | FASTER | Documentation, Uses, and more | ||||
| kronatools | FASTER | Documentation, Uses, and more | ||||
| kubernetes/expanse | Expanse | Documentation, Uses, and more | ||||
| lame | ACES FASTER |
LAME is a high-quality MPEG Audio Layer III (MP3) encoder licensed under the GNU Lesser General Public License (LGPL). It is considered one of the best MP3 encoders available. | Audio Encoding, Mp3, Open-Source | Other Engineering & Technologies | Encoder | Documentation, Uses, and more |
| lammps | ACES Anvil Bridges-2 Delta DeltaAI FASTER Ookami Stampede3 |
LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code designed for simulating large-scale atomistic systems. It is highly versatile and can be used to model a wide range of materials and complex molecular structures. | Molecular Dynamics, Simulation, Computational Chemistry | Physical Chemistry, Chemical Sciences | Code/Package | Documentation, Uses, and more |
| lapack | FASTER Ookami |
LAPACK (Linear Algebra PACKage) is a software library for numerical linear algebra that provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. | Numerical Linear Algebra, Software Library, Mathematics | Mathematics,Engineering, Mathematics | Library | Documentation, Uses, and more |
| lasso-python | ACES | Lasso-python is a Python library that provides tools for lasso regression, a linear regression technique that performs variable selection and regularization to improve the model's prediction and interpretability. | Python Library, Machine Learning, Regression Analysis | Statistics & Probability, Mathematics | Library | Documentation, Uses, and more |
| last | FASTER | Last is a program for aligning sequencing reads to a reference genome with important applications in the field of bioinformatics. | Bioinformatics, Sequence Alignment, Genomics | Documentation, Uses, and more | ||
| lastz | FASTER | Lastz is a program for aligning DNA sequences, a key step in comparative genomics analysis. It efficiently finds local alignments between sequences, identifying areas of similarity and potential evolutionary relationships. | Bioinformatics, DNA Sequencing, Alignment, Comparative Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| latex | FASTER | LaTeX is a typesetting system commonly used for scientific and technical documentation preparation. It is widely used for the communication and publication of scientific documents in fields such as mathematics, computer science, physics, engineering, and more. | Typesetting, Scientific Communication, Document Preparation | Natural Sciences, Mathematics, Computer & Information Sciences, Engineering & Technology | Publishing | Documentation, Uses, and more |
| launcher | Anvil | Launcher is a software application that provides a centralized platform for accessing and managing various files, programs, and tools on a computer system. It serves as a customizable tool for organizing shortcuts and quick access to frequently used resources. | Software Management, File Organization, Shortcut Access | System Tool | Documentation, Uses, and more | |
| lazygit | Bridges-2 | lazygit is a simple terminal UI for git commands, with the ability to easily view and manage changes in repositories. | Version Control, Git, Terminal Ui, Software Development | Engineering & Technology | Tools | Documentation, Uses, and more |
| lddt | FASTER | lddt (Local Dynamic Data race Tester) is a tool for testing and debugging data races in parallel programs. | Testing, Debugging, Parallel Programming | Computer Science, Computer & Information Sciences | Testing & Debugging Tool | Documentation, Uses, and more |
| learning | Anvil | Documentation, Uses, and more | ||||
| leidenalg | FASTER | Documentation, Uses, and more | ||||
| leptonica | ACES Delta FASTER |
Leptonica is an open-source image processing and image analysis library. It provides a wide range of image processing functions and is used for tasks such as image enhancement, binarization, morphology, and more. Leptonica is written in C and provides bindings for various programming languages. | Image Processing, Image Analysis, Open-Source, Library, C | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| lerc | ACES FASTER |
LERC (Limited Error Raster Compression) is an algorithm for raster data compression that provides high compression ratios with minimal loss in data quality. It is commonly used in geospatial applications to reduce storage space and transmission times for large raster datasets. | Compression, Raster Data, Geospatial Applications | Earth & Environmental Sciences, Other Natural Sciences | Algorithm | Documentation, Uses, and more |
| leveldb | ACES FASTER |
LevelDB is a fast key-value storage library designed by Google that provides an ordered mapping from string keys to string values. It has features like high performance, low latency reads, low write amplification, data compression, and automatic data compaction. LevelDB is written in C++ and is optimized for use in embedded systems and applications requiring persistent storage. | Storage, Database | Computer & Information Sciences | Library | Documentation, Uses, and more |
| levmar | FASTER | Documentation, Uses, and more | ||||
| lftp | FASTER | Documentation, Uses, and more | ||||
| lhsmdu | FASTER | LHSMDU (Latin Hypercube Sampling Multivariate Data Uncertainty) is a Python library for generating Latin hypercube samples with multivariate data uncertainty. Latin hypercube sampling is a statistical method for generating a sample of plausible scenarios by dividing the input variables into equally probable intervals and sampling once from each interval. LHSMDU extends this concept to incorporate uncertainty in the multivariate data. | Latin Hypercube Sampling, Multivariate Data, Uncertainty Quantification, Statistical Sampling, Python Library | Other Mathematics | Python Library | Documentation, Uses, and more |
| libaec | ACES FASTER |
libaec is a C library for lossless image compression. | Image Compression, Lossless Compression | Computer & Information Sciences | Compression | Documentation, Uses, and more |
| libaio | ACES Delta FASTER KyRIC |
libaio is a library that provides a Linux-native asynchronous I/O facility to applications. It allows applications to perform I/O operations without being blocked, thus improving performance by enabling concurrent I/O operations. | I/O Library, Linux Library, Asynchronous I/O | Computer & Information Sciences | Operating System Library | Documentation, Uses, and more |
| libarchive | ACES FASTER |
libarchive is a programming library that can create and read several different streaming archive formats, including most popular tar variants, cpio, and zip. It can also write entry content directly to or read entry content directly from memory, and provides hooks to read and write the entry content as it is processed. Program is available in C and C++. | Programming Library, Archive, Compression, Data Management | Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| libassuan | ACES | Documentation, Uses, and more | ||||
| libatomic_ops | ACES FASTER |
Libatomic_ops is a library implementing atomic memory access operations for use in concurrent programming. It provides a number of low-level memory access and synchronization operations which can be used in lock-free data structures and for inter-thread communication without the need for locks. | Concurrent Programming, Atomic Operations, Memory Access, Synchronization | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libavif | FASTER | Documentation, Uses, and more | ||||
| libbigwig | FASTER | Documentation, Uses, and more | ||||
| libbsd | Anvil Delta DeltaAI KyRIC |
libbsd is a library that provides functions typically found in the BSD operating systems. It aims to offer a more portable solution for developers needing BSD functions on non-BSD systems. | Library, Bsd, Operating System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libcap-devel | Ookami | The libcap-devel package contains the development files and documentation for the libcap library. This library implements the user-space interfaces to the POSIX 1003.1e capabilities available in Linux kernels. | Library, Development, Documentation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libcdms | FASTER | libcdms is a computational software library for climate and atmospheric sciences, specifically designed for the analysis, management, and visualization of climate datasets. | Climate Science, Atmospheric Sciences, Data Management, Visualization | Atmospheric Sciences, Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| libcerf | ACES DeltaAI FASTER |
libcerf is a C library that provides efficient and accurate implementations of complex error functions, along with Dawson, Fresnel, and Voigt functions. The library is designed to facilitate the computation of complex error functions for a wide range of applications in scientific computing. | Error Functions, Scientific Computing, C Library | Mathematics | Library | Documentation, Uses, and more |
| libcifpp | FASTER | libcifpp is a C++ library for reading, writing, and manipulating Crystallographic Information Format (CIF) files. CIF is a standard text file format for representing crystallographic information approved by the International Union of Crystallography. | Cif Files, Crystallography, Library, C++ | Documentation, Uses, and more | ||
| libcircle | FASTER | Documentation, Uses, and more | ||||
| libdap | ACES FASTER |
The libdap (Data Access Protocol) library is a software package that provides an implementation of DAP (Data Access Protocol) for accessing and sharing scientific data over the internet. DAP is a protocol that allows users to access and query remote data repositories in a unified and standardized manner. | Data Access, Scientific Data, Internet Protocol | Other Computer & Information Sciences | Data Access | Documentation, Uses, and more |
| libdeflate | ACES FASTER |
libdeflate is a library for fast, flexible, and memory-efficient DEFLATE-based compressed data decompression. | Compression, Data Decompression | Computer & Information Sciences | Compression | Documentation, Uses, and more |
| libdicom | FASTER | Documentation, Uses, and more | ||||
| libdivsufsort | ACES | Documentation, Uses, and more | ||||
| libdrm | ACES FASTER |
Direct Rendering Manager (DRM) library for interacting with kernel mode-setting (KMS) drivers, particularly the Direct Rendering Infrastructure (DRI) modules in the Linux kernel. | Graphics, Linux, Kernel, Driver | Documentation, Uses, and more | ||
| libdrs | FASTER | libdrs is a Python library for Differential RNA-seq (Differential RNA sequencing) analysis. It provides various tools for the analysis of gene expression data generated from RNA-seq experiments, focusing on identifying differentially expressed genes between different conditions or treatments. | Python Library, RNA-Seq Analysis, Gene Expression Analysis | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| libedit | KyRIC | libedit is an open-source library that provides a readline-like interface for line editing in command-line applications. It is a replacement for GNU Readline used in many Unix-like systems, providing similar functionality but with a more permissive open-source license (BSD-style license). | Library, Command-Line, Line Editing, History, Open-Source | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| libepoxy | ACES FASTER |
libepoxy is a library for handling OpenGL function pointer management. It makes it easy to call OpenGL functions and to know when extensions are available. | Opengl, Library, Graphics | Computer & Information Sciences | Development | Documentation, Uses, and more |
| libev | ACES FASTER |
libev is a high-performance event loop that provides a full-featured alternative to the event loop provided by the standard C library. It is designed for high scalability and low latency applications. | Event Loop, High Performance, Scalable, Low Latency, Operating System Independent | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libevent | ACES FASTER KyRIC |
libevent is a robust event notification library that provides a mechanism to execute a callback function when specific events occur on a file descriptor or after a timeout has been reached. It is designed to be highly efficient and versatile, capable of handling various types of events in a scalable manner. | Event Notification, Callback Functions, Scalable, Efficient | Computer & Information Sciences | Development | Documentation, Uses, and more |
| libfabric | ACES Anvil Delta DeltaAI FASTER KyRIC Ookami |
libfabric is a high-performance library for fabric interfaces, designed to abstract fabric communication resources to applications while providing flexibility to applications that need to bypass the fabric interfaces. It provides fabric-agnostic interfaces for communication in high-performance computing (HPC) environments. | Fabric Interfaces, High-Performance Computing, Communication Resources | Computer Science, Engineering & Technology | Communication Library | Documentation, Uses, and more |
| libffi | ACES Anvil Delta DeltaAI FASTER KyRIC Ookami |
libffi is a library that provides a portable, high-level programming interface to various calling conventions. It allows a C function to be called from a language other than C without having to hand-write assembly code. | Library, Portability, Calling Conventions | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| libflame | Anvil FASTER |
libflame is a portable library for dense matrix computations, providing high-performance implementations of the BLAS and LAPACK interfaces. | Linear Algebra, Matrix Computations, Numerical Computation | Applied Mathematics, Mathematics | Numerical Computing | Documentation, Uses, and more |
| libfontenc | DeltaAI | Documentation, Uses, and more | ||||
| libfyaml | ACES FASTER |
Documentation, Uses, and more | ||||
| libgcrypt | ACES FASTER |
Libgcrypt is a general-purpose cryptographic library originally based on code from GnuPG. It provides various cryptographic algorithms to secure data and communications. | Cryptography, Security, Encryption | Computer Science, Computer & Information Sciences | Cryptographic Library | Documentation, Uses, and more |
| libgd | ACES DeltaAI FASTER Ookami |
Libgd is an open-source graphics library. It allows your code to quickly draw images complete with lines, arcs, text, multiple colors, cut and paste from other images, and flood fills. It can generate WBMP files on the fly. It is also compatible with PHP. | Graphics Library, Image Manipulation, Php Library | Other Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| libgeotiff | ACES DeltaAI FASTER |
Libgeotiff is a library for reading and writing coordinate system information embedded in geotiff files. | Geotiff, Metadata, Coordinates, Geospatial | Earth & Environmental Sciences | File Handling | Documentation, Uses, and more |
| libgit2 | ACES FASTER Ookami |
libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings. | Version Control System, Git, Library | Computer & Information Sciences | Version Control System | Documentation, Uses, and more |
| libglu | ACES FASTER |
libglu is a software library that provides support for building OpenGL applications. It is designed to complement the functionality provided by OpenGL and aids in handling complex geometric shapes, tessellation, and creating polygonal models. | Software Library, Geometry Processing, Computer Graphics | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libglvnd | ACES FASTER |
libglvnd is the open-source implementation of the vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors' graphics drivers and the X server. | Graphics, Opengl, Vendor-Neutral Dispatch | Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| libgpg-error | ACES FASTER KyRIC |
Libgpg-error is a small library that defines common error values for all GnuPG components. It is used by GnuPG and some other packages. | Error Handling, Library, Gnupg | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libgpuarray | ACES FASTER |
libgpuarray is a library that provides a common, numpy-like array object to represent GPU data for array-oriented algorithms in Python. It is designed to work with various libraries whose primary focus is on GPU acceleration, such as Theano or PyCUDA. | Gpu Acceleration, Array-Oriented Algorithms, Python Library | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| libharu | FASTER | libHaru is a free, open-source software library for generating PDF files. It supports a wide range of features for creating PDF documents programmatically, including text, images, vector graphics, and more. | Pdf Generation, Open-Source Software, Programming Library | Computer & Information Sciences | Pdf Generation | Documentation, Uses, and more |
| libice | Delta | libice is a library that provides support for Inter-Client Exchange (ICE) in the X Window System, allowing X clients to securely exchange data through the X server. | Library, Inter-Client Exchange, X Window System | Computer & Information Sciences | Communication | Documentation, Uses, and more |
| libiconv | ACES Anvil FASTER KyRIC |
libiconv is a library that provides character set conversion support. It converts text data between different character encoding schemes. | Character Set Conversion, Text Data, Encoding | Other Computer & Information Sciences, Computer & Information Sciences | Conversion Tool | Documentation, Uses, and more |
| libidn | ACES FASTER |
Libidn is an internationalized domain name library designed to help with the process of converting internationalized domain names to/from ASCII representation. It implements the Stringprep, Punycode and IDNA specifications defined by the IETF (Internet Engineering Task Force). | Software Library, Internationalization, Domain Names | Computer & Information Sciences | Dynamic Link Library (Dll) | Documentation, Uses, and more |
| libidn2 | ACES DeltaAI FASTER KyRIC |
Libidn2 is a library that implements the Stringprep, Punycode and IDNA specifications defined by the IETF Internationalized Domain Names (IDN) working group. | Domain Names, Idns, Stringprep, Punycode | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libint | ACES FASTER |
libint is a library for the evaluation of molecular integrals needed in computational chemistry and related fields. It provides efficient and accurate implementations for various types of integrals used in quantum chemistry calculations. | Computational Chemistry, Molecular Integrals, Quantum Chemistry | Physical Chemistry, Chemical Sciences | Computational | Documentation, Uses, and more |
| libjpeg | Delta | libjpeg is a widely-used open-source library for reading and writing images in JPEG format. It provides functions for compression and decompression of JPEG images, making it a valuable tool for handling image files in various applications. | Image Processing, Compression, Library | Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libjpeg-turbo | ACES DeltaAI FASTER |
libjpeg-turbo is a high-speed version of the widely-used JPEG image compression library. It uses SIMD instructions to accelerate JPEG compression and decompression on x86, x86-64, and ARM processors. | Image Compression, Jpeg Compression, Library, Open Source | Computer & Information Sciences | Compression Library | Documentation, Uses, and more |
| libmad | ACES FASTER |
Documentation, Uses, and more | ||||
| libmatheval | FASTER | Libmatheval is a library for evaluating mathematical expressions on the fly. It supports a wide range of mathematical functions and operations, making it a versatile tool for numerical computations and symbolic manipulation. | Mathematical Expression Evaluation, Mathematical Functions, Symbolic Manipulation | Other Mathematics | Computational Software | Documentation, Uses, and more |
| libmbd | FASTER | Documentation, Uses, and more | ||||
| libmd | Anvil Delta DeltaAI |
libmd is a library for molecular dynamics simulations that allows for the integration of equations of motion for particles interacting with different potentials. | Molecular Dynamics, Simulation, Library | Physical Sciences | Computational | Documentation, Uses, and more |
| libmesh | Anvil FASTER Stampede3 |
Libmesh is a C++ finite element library designed to provide a framework for the numerical simulation of partial differential equations in high dimensions. It supports 1D, 2D, and 3D mesh generation, provides a wide range of finite element types, and includes solvers for various types of PDEs. | Finite Element Library, Numerical Simulation, Partial Differential Equations | Other Mathematics | Library | Documentation, Uses, and more |
| libnotify | Ookami | libnotify is a library that provides a way to display desktop notifications to users. It is typically used by desktop environments such as GNOME to show notifications for various events and applications. | Notifications, Desktop, Library | Other Computer & Information Sciences | System Software | Documentation, Uses, and more |
| libnsl | ACES Delta FASTER |
The libnsl library provides an interface for applications to make use of the services provided by the Network Services Layer (NSL). It offers functions that allow applications to communicate over the network using a variety of protocols. | Network Services, Communication, Protocols | Computer & Information Sciences | System Software | Documentation, Uses, and more |
| libogg | ACES FASTER |
Libogg is a reference implementation of the Ogg bitstream format. It provides a simple, low-level API for working with Ogg bitstreams. | Library, Bitstream, Audio | Computer & Information Sciences | Data Format | Documentation, Uses, and more |
| libopus | ACES FASTER |
libopus is a high-quality audio codec that is specifically designed for interactive speech and audio transmission over the Internet. It is part of the wider Opus audio codec family, covering a wide range of bitrates and applications. | Audio Codec, Real-Time Communication, Internet Transmission | Engineering & Technology | Documentation, Uses, and more | |
| libpals | Delta | Libpals is a collection of tools for analyzing and manipulating phylogenetic trees. It provides functionalities for tree comparison, consensus tree construction, tree visualization, and more. | Phylogenetics, Bioinformatics, Computational Biology | Systematics & Population Biology, Biological Sciences | Library | Documentation, Uses, and more |
| libpciaccess | ACES FASTER KyRIC |
libpciaccess is a library providing generic access to the PCI bus and devices for use in user-space programs. It allows user-space drivers to directly map PCI memory regions, perform bus transactions, and query devices on the PCI bus. | Library, Pci Bus Access, User-Space Drivers | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libpng | ACES Anvil Delta DeltaAI FASTER Ookami |
Libpng is the official PNG reference library, used to support the PNG (Portable Network Graphics) format for storing raster images. It provides a set of functions for creating, reading, and manipulating PNG image files. | Image Processing, Graphics Library, Raster Images | Computer & Information Sciences | Data Handling | Documentation, Uses, and more |
| libpressio | ACES | Documentation, Uses, and more | ||||
| libpsl | ACES FASTER |
Libpsl is a C library that provides functions to work with the Public Suffix List (PSL), which is a database of domain suffixes (like .com, .co.uk, etc.) that are under public registry control. | C Library, Domain Management, Public Suffix List | Computer & Information Sciences | System/Library Software | Documentation, Uses, and more |
| libpthread-stubs | Anvil DeltaAI FASTER |
Documentation, Uses, and more | ||||
| libreadline | ACES FASTER |
libreadline is a GNU library that provides line-editing capabilities for interactive programs with a command-line interface. It allows users to edit text as they type commands, providing features such as history, editing, and completion of input. | Command-Line Interface, Text Editing, Gnu Library, Interactive Programs | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| librmath | FASTER | Documentation, Uses, and more | ||||
| librom | ACES FASTER |
LibROM is a library for Reduced Order Models (ROMs) that provides tools for model reduction of complex systems in engineering and computational science applications. It offers a range of algorithms and methods to reduce the computational cost of high-fidelity simulations. | Software Library, Model Reduction, Computational Science | Engineering & Technology | Model Reduction Tool | Documentation, Uses, and more |
| librosa | ACES FASTER |
Documentation, Uses, and more | ||||
| librsvg | ACES FASTER |
Librsvg is a free software library to render SVG files and convert them to other formats using the Cairo rendering engine. | Software Library, Free Software, Svg Rendering, File Conversion | Computer & Information Sciences | Rendering & Conversion | Documentation, Uses, and more |
| librttopo | ACES FASTER |
librttopo is a tool for computational topology focusing on persistent homology and topological data analysis. | Computational Topology, Persistent Homology, Topological Data Analysis | Mathematics | Computational Software | Documentation, Uses, and more |
| libsais | FASTER | Documentation, Uses, and more | ||||
| libsci | Delta DeltaAI |
libsci is a library of optimized scientific routines for high-performance computing (HPC) environments. It provides a collection of mathematical functions and computational kernels tailored for scientific and engineering applications that require high computational efficiency. | Hpc, Scientific Computing, Optimization | Other Mathematics | Mathematics/Computational Software | Documentation, Uses, and more |
| libsci_acc | DeltaAI | Documentation, Uses, and more | ||||
| libseccomp | ACES KyRIC |
Libseccomp is an open-source library that provides an easy-to-use, platform-independent interface for working with the Linux Kernel's syscall filtering mechanism. It allows developers to filter system calls made by an application, restricting the actions the application can perform at the kernel level. | Syscall Filtering, Linux Kernel, Security | Computer & Information Sciences | Development | Documentation, Uses, and more |
| libsharp2 | ACES FASTER |
Documentation, Uses, and more | ||||
| libsigc++ | FASTER | Documentation, Uses, and more | ||||
| libsigsegv | FASTER KyRIC |
libsigsegv is a library for handling page faults in user mode. It provides a convenient and efficient way to establish a handler for memory violations while exploring memory areas. | Library, Memory, Page Fault | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| libsm | Delta | Libsm is a library that provides a set of common utilities for scientific computing in C++. | Library, Scientific Computing, C++ | Other Natural Sciences | Library | Documentation, Uses, and more |
| libsndfile | ACES Delta FASTER |
libsndfile is a C library for reading and writing files containing sampled sound (such as WAV, AIFF, and AU) through one standard interface. | Audio Processing, File Input/Output, C Library, Audio File Formats | Other Natural Sciences | Audio Processing | Documentation, Uses, and more |
| libsodium | ACES FASTER |
libsodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing, and more. It is a portable, cross-compilable, installable, packageable fork of NaCl, a highly respected cryptographic library developed by Daniel J. Bernstein. | Cryptography, Security, Encryption, Password Hashing | Computer & Information Sciences | Cryptography | Documentation, Uses, and more |
| libsoup | ACES FASTER |
libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications. Features include asynchronous I/O using GMainContext and WebSockets support. | Http, Client/Server, Gnome, Gobjects, Asynchronous I/O, Websockets | Computer Science, Computer & Information Sciences | Http Client/Server Library | Documentation, Uses, and more |
| libspatialindex | ACES FASTER |
Libspatialindex is an open-source library for spatial indexing methods, designed to provide various spatial index structures which can be used for spatial queries in databases or applications. | Spatial Index, Library, Open-Source | Computer Science, Computer & Information Sciences | Data Processing/Management | Documentation, Uses, and more |
| libspatialite | ACES FASTER |
libspatialite is an open-source library that extends the core SQLite database engine with spatial SQL capabilities. It allows users to create, manage, and query spatial data in a SQLite database, providing support for spatial functions and geometric data types. | Spatialite, Geospatial, Database, Spatial Data | Computer & Information Sciences | Database Management | Documentation, Uses, and more |
| libssh | FASTER | libssh is a multiplatform C library implementing the SSHv2 protocol on client and server side. It provides a stable API, high performance, and is designed to be easy to use. | Ssh, Library, Networking | Computer & Information Sciences | Networking | Documentation, Uses, and more |
| libstdcompat | ACES | Documentation, Uses, and more | ||||
| libsvm | FASTER | Documentation, Uses, and more | ||||
| libszip | Anvil | libszip is a compression library for large datasets used in scientific computing and research. It provides support for efficient and high-speed compression and decompression of large data files, particularly in formats commonly used in scientific applications. | Compression Library, Scientific Computing, Data Compression, Research Tools | Other Natural Sciences | Compression | Documentation, Uses, and more |
| libtasn1 | ACES FASTER |
libtasn1 is a library developed for ASN.1 and DER manipulation. ASN.1 is a standard interface description language for defining data structures that can be serialized and deserialized in a cross-platform way. | Library, Asn.1, Der, Serialization, Deserialization | Computer Science, Computer & Information Sciences | Development Library | Documentation, Uses, and more |
| libtiff | ACES Anvil DeltaAI FASTER |
libtiff is a library for reading and writing TIFF (Tagged Image File Format) files. It provides support for handling images and documents in various uncompressed and compressed formats. | Image Processing, File Format, Library, Tiff, Image Storage | Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libtirpc | ACES Anvil Delta Expanse FASTER |
libtirpc is an open-source library that provides an implementation of Sun's Transport-Independent RPC (TI-RPC) protocol. | Software Library | Computer & Information Sciences | Development | Documentation, Uses, and more |
| libtool | ACES DeltaAI FASTER KyRIC |
Libtool is a generic library support script that manages the creation of static and dynamic libraries on various Unix-like operating systems. | Library Management, Software Development, Compilation | Engineering & Technology | Utility/Tool | Documentation, Uses, and more |
| libunistring | ACES DeltaAI FASTER KyRIC |
libunistring is a C library that provides functions to manipulate Unicode strings and includes functions for encoding conversion, case mapping, normalization, and more. | Unicode, Encoding, String Manipulation, Localization | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| libunwind | ACES Delta DeltaAI FASTER Ookami |
libunwind is a portable and efficient C programming interface (API) to determine the call-chain of a program. It is primarily used for debugging, performance profiling, and runtime instrumentation. | Debugging, Profiling, Runtime Instrumentation, Call Stack, C Programming | Engineering & Technology | Development | Documentation, Uses, and more |
| libv8 | Anvil | libv8 is an open-source C++ library that provides a fast and efficient JavaScript engine for embedding in various applications and tools. | Javascript Engine, C++ Library | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| libvdwxc | ACES FASTER |
Documentation, Uses, and more | ||||
| libvorbis | ACES FASTER |
Libvorbis is a free and open-source software library for encoding and decoding audio data compressed with the Vorbis audio codec. It is part of the Xiph.org Foundation's Ogg project and is used for high-quality audio compression. | Audio Codec, Compression, Open-Source | Engineering & Technology | Audio Processing | Documentation, Uses, and more |
| libvori | ACES FASTER |
libvori is a library for calculating voronoi diagrams. It provides functions for generating voronoi diagrams from a set of points in the plane. | Voronoi Diagrams, Computational Geometry, Library | Other Mathematics, Mathematics | Calculation Tool | Documentation, Uses, and more |
| libwebp | ACES FASTER |
libwebp is a library for working with the WebP image format. It provides tools to encode, decode, and manipulate images in the WebP format, which is a modern image format that provides both lossy and lossless compression for images on the web. | Image Processing, Compression, Web Development, Library | Other Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| libwnck | FASTER | Documentation, Uses, and more | ||||
| libwpe | ACES FASTER |
libwpe is a library that provides web platform support for Wayland compositors and other clients that need web content rendered on a Wayland surface. | Library, Web Platform Support, Wayland Compositors, Web Content Rendering | Computer & Information Sciences | Library | Documentation, Uses, and more |
| libx11 | Anvil Delta DeltaAI |
libX11 is the X Window System protocol client library which provides an interface to the X Window System core protocol and provides higher-level functions for building window systems on top of the X Window System core. | X Window System, Client Library, Window System Interface, Graphics | Computer & Information Sciences, Computer Science | Software Development | Documentation, Uses, and more |
| libx265 | Delta | Documentation, Uses, and more | ||||
| libxau | Anvil Delta DeltaAI FASTER |
libXau is a library that provides authentication data for Xlib-based client programs. | Library, Authentication, Xlib | Computer & Information Sciences | Documentation, Uses, and more | |
| libxaw | Delta | Documentation, Uses, and more | ||||
| libxc | ACES FASTER Ookami Stampede3 |
LibXC is a library of exchange-correlation functionals for density-functional theory. | Quantum Mechanics, Computational Chemistry | Chemical Sciences | Density Functional Theory | Documentation, Uses, and more |
| libxcb | Anvil Delta DeltaAI FASTER |
libxcb is a C language library for the X Window System's X protocol, providing a replacement for the traditional Xlib API. It allows for more efficient communication between X clients and the X server by reducing round-trip requests. | X Window System, C Library, X Protocol | Computer Science, Computer & Information Sciences | Programming | Documentation, Uses, and more |
| libxcrypt | DeltaAI | Documentation, Uses, and more | ||||
| libxdmcp | Anvil Delta DeltaAI FASTER |
libxdmcp is the X Display Manager Control Protocol library. It provides an API for the X Display Manager Control Protocol (XDMCP) for both the client and server side. | X11, Display Manager, Network Protocol | Computer & Information Sciences | Networking | Documentation, Uses, and more |
| libxext | Anvil | Documentation, Uses, and more | ||||
| libxfce4ui | FASTER | Documentation, Uses, and more | ||||
| libxfce4util | FASTER | Documentation, Uses, and more | ||||
| libxfont | DeltaAI | Documentation, Uses, and more | ||||
| libxml++ | FASTER | Documentation, Uses, and more | ||||
| libxml2 | ACES Anvil DeltaAI FASTER KyRIC |
Libxml2 is a software library for parsing, validating, and manipulating XML and HTML documents. It provides a tree-based API for working with XML data and supports various standards such as XML 1.0, XPath, XInclude, XPointer, and XML Catalogs. | Xml, Html, Parsing, Validation, Manipulation | Computer & Information Sciences | Parsing | Documentation, Uses, and more |
| libxp | Delta DeltaAI |
Documentation, Uses, and more | ||||
| libxpm | DeltaAI | Documentation, Uses, and more | ||||
| libxrender | Anvil | Documentation, Uses, and more | ||||
| libxscrnsaver | Anvil | libxscrnsaver is a library that provides an X Window System client interface to the X11 MIT-SCREEN-SAVER extension. It allows applications to inhibit the screensaver and screen blanking in a standardized way. | Library, X Window System, Screensaver, Screen Blanking | Computer & Information Sciences | System Library | Documentation, Uses, and more |
| libxslt | ACES Anvil FASTER |
Libxslt is the XSLT C library developed for the GNOME project. It is used for transforming XML documents into other formats using XSLT stylesheets. Libxslt is based on libxml2, the XML C parser and toolkit. | Xml, Xslt, C Library, Transformation | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| libxsmm | ACES FASTER |
libxsmm is a library for small, dense matrix-matrix multiplications developed for modern CPUs. It provides high performance on Intel Architecture CPUs and comes with different optimized code paths tailored for different processor microarchitectures. | Library, Matrix Multiplication, Intel Cpus | Computer & Information Sciences | Optimization Library | Documentation, Uses, and more |
| libxt | Delta | Libxt is a library offering extensions for automating compilation, dependency tracking, and execution of computational tasks within HPC environments. | Library, Hpc, Automation, Compilation, Dependency Tracking, Parallel Processing | Engineering & Technology | Library | Documentation, Uses, and more |
| libyaml | ACES FASTER |
LibYAML is a YAML 1.1 parser and emitter written in C. It is a library for parsing and emitting YAML data. YAML is a human-readable data serialization format that is commonly used for configuration files and data exchange between languages. LibYAML allows developers to integrate YAML support into their applications. | Yaml, Parser, Emitter, Serialization, Configuration | Computer & Information Sciences, Engineering & Technology | Parsing/Serialization | Documentation, Uses, and more |
| libzip | ACES FASTER |
libzip is a C library for reading, creating, and modifying zip archives. It provides a simple programming interface for managing zip files. | C Library, Zip Archives, File Management | Computer & Information Sciences | Compression | Documentation, Uses, and more |
| lifelines | ACES | Lifelines is a Python library for survival analysis, reliability, and lifetime data analysis. It provides tools for data preprocessing, estimating survival functions, hazard rates, and confidence intervals, as well as modeling, predicting, and visualizing survival data. | Python Library, Survival Analysis, Lifetime Data Analysis, Reliability Analysis, Data Visualization | Statistics & Probability | Python Library | Documentation, Uses, and more |
| liftoff | FASTER | Liftoff is a powerful build system for iOS and macOS projects. It is designed to be faster and more reliable than the built-in Xcode build system, providing a more efficient development experience for Apple platform developers. | Build System, Ios Development, Macos Development, Software Development, Apple Platforms | Engineering & Technology | Build Automation | Documentation, Uses, and more |
| likwid | FASTER KyRIC Ookami |
LIKWID is a performance analysis tool suite designed to support HPC/PCP (performance counter profiling) on Intel and AMD processors. It offers a set of command-line tools and libraries that facilitate the collection of performance data and analysis on modern hardware architectures. | Performance Analysis, Hpc, Performance Counter Profiling, Hardware Performance Counters | Performance Evaluation & Benchmarking, Engineering & Technology | Tool | Documentation, Uses, and more |
| linaro | Ookami | Linaro is a collaborative engineering organization that works on consolidating and optimizing open-source software for the Arm architecture, including the Linux kernel, toolchain, and graphics stack. | Collaborative Engineering, Arm Architecture, Open-Source Software Optimization | Computer Information Sciences | Development & Optimization Tools | Documentation, Uses, and more |
| links | FASTER | Links is a text-based web browser with support for rendering tables and frames, background downloading, font styles, colors, and SSL connections. It is customizable and highly configurable for browsing the web in a terminal or console environment. | Web Browser, Text-Based, Console-Based, Terminal-Based | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| lis | FASTER | Documentation, Uses, and more | ||||
| lit | FASTER | Documentation, Uses, and more | ||||
| littlecms | ACES FASTER |
LittleCMS is a color management engine that provides simplified and portable fundamentals for the development and integration of color management components into various software applications. | Color Management, Software Development, Image Processing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| lldb | Ookami | LLDB is a powerful and modern debugger for C, C++, and Objective-C languages. It is part of the LLVM project and mainly used for debugging programs on macOS and iOS. | Debugger, Llvm, C/C++, Objective-C | Computer Science, Computer & Information Sciences | Debugger | Documentation, Uses, and more |
| llvm | ACES Delta FASTER Ookami |
The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. LLVM is used for developing compiler back-ends, static analysis tools, and JIT compilation engines. | Compiler, Toolchain | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| lmdb | ACES FASTER |
LMDB is an extremely fast, memory-efficient and crash-proof key-value store that is well-suited for embedded applications and high-performance web services. It is written in C and operates directly on memory-mapped files. | Database, Key-Value Store, Memory-Mapped Files | Computer & Information Sciences | Database Management System | Documentation, Uses, and more |
| lmfit | FASTER | Documentation, Uses, and more | ||||
| lmod | ACES Bridges-2 Delta DeltaAI FASTER Stampede3 |
Lmod is an environment module system that helps users manage their software environment by providing a convenient way to dynamically modify the user's environment through modulefiles. It supports multiple collections of modules that can be easily swapped in and out, allowing users to load the software packages and versions they need for their work. | Module Management, Software Environment, Environment Module System | Infrastructure & Instrumentation, Engineering & Technology | Utility | Documentation, Uses, and more |
| log4cpp | FASTER | Documentation, Uses, and more | ||||
| longestrunsubsequence | FASTER | Documentation, Uses, and more | ||||
| longqc | FASTER | LongQC is a quality control tool for long-read sequencing data, designed specifically for third-generation sequencing technologies like Pacific Biosciences (PacBio) and Oxford Nanopore Technologies. It aims to assess the quality of raw long-read sequencing data and provide users with detailed insights into the characteristics of the sequenced reads. | Quality Control, Long-Read Sequencing, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| loopy | FASTER | Loopy is a software tool for array-oriented programming with multiple inputs and outputs, offering automatic differentiation and GPU support. It enables users to express and solve linear equations in a highly optimized manner. | Programming, Optimization, Linear Algebra, Automatic Differentiation | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| lowcharts | Bridges-2 | Lowcharts is a Python library for creating basic low-level charts with a simplistic and minimalistic interface. It aims to provide users with an easy-to-use tool for generating simple line charts, bar charts, and scatter plots. | Python Library, Data Visualization, Charting Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| lpsolve | ACES FASTER |
Documentation, Uses, and more | ||||
| ls-dyna | FASTER | Documentation, Uses, and more | ||||
| ls-opt | FASTER | Documentation, Uses, and more | ||||
| ls-prepost | FASTER | Documentation, Uses, and more | ||||
| ls-tasc | FASTER | Documentation, Uses, and more | ||||
| lsd2 | FASTER | Documentation, Uses, and more | ||||
| ltr_retriever | FASTER | Documentation, Uses, and more | ||||
| lua | ACES Expanse FASTER Ookami |
Lua is a lightweight, high-level, multi-paradigm programming language designed for embedded use in applications. It is known for its simplicity, efficiency, and flexibility. | Programming Language, Scripting Language, Embedded Systems | Computer & Information Sciences | Documentation, Uses, and more | |
| luajit | Expanse Ookami |
Documentation, Uses, and more | ||||
| lumpy | FASTER | Lumpy is a structural variant caller that can detect various types of genomic variations using paired-end short reads, such as deletions, insertions, inversions, and duplications. It provides insights into the structural organization of a genome. | Genomic Analysis, Structural Variant Detection | Genomics, Biological Sciences | Variant Caller | Documentation, Uses, and more |
| lvm2 | KyRIC | Logical Volume Manager 2 (LVM2) is a system tool for managing logical volumes. It is typically used to manage disk storage space in a more flexible manner than traditional partitioning. | System Tool, Storage Management, Disk Management | Engineering & Technology | Utility | Documentation, Uses, and more |
| lwgrp | FASTER | Documentation, Uses, and more | ||||
| lxml | ACES FASTER |
lxml is a powerful and feature-rich library for processing XML and HTML in Python. It provides a simple and pythonic API for efficient handling of XML and HTML data. | Python Library, Xml Processing, Html Processing, Data Parsing | Computer & Information Sciences, Other Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| lz4 | ACES FASTER Ookami |
LZ4 is a lossless data compression algorithm that offers extremely fast compression and decompression speeds. It is designed to be very efficient in terms of both processing power and memory usage. | Compression, Data Compression, Lossless Compression | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| lzma | Delta | LZMA is a high-compression data compression software program that employs the Lempel-Ziv-Markov chain algorithm (LZMA). It provides lossless data compression and decompression algorithms. | Compression, Data Compression, Algorithm | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| lzo | ACES FASTER |
Lempel-Ziv-Oberhumer (LZO) is a data compression algorithm that focuses on high-speed compression and decompression. It offers fast compression and decompression speeds with moderate compression ratios. LZO is commonly used in applications where speed is more critical than achieving the highest compression ratios. | Data Compression, Algorithm, High-Speed | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| m4 | ACES DeltaAI FASTER KyRIC |
m4 is a general-purpose macro processor designed to be used with any programming language or data file format. It is commonly used to generate source code or text files and is often used as part of the build process for software development. | Macro Processor, Text Processing, Software Development, Build Process | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| mach | FASTER | Documentation, Uses, and more | ||||
| macs2 | FASTER | Model-based Analysis of ChIP-Seq (MACS) version 2 is a tool for identifying transcription factor binding sites and histone modification enrichment from ChIP-Seq data. It uses a dynamic Poisson distribution to effectively capture local biases in the genome while comparing the tag position density profiles between ChIP-Seq data and control samples. | Chip-Seq Analysis, Transcription Factor Binding Sites, Histone Modification, Bioinformatics | Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| maeparser | ACES FASTER |
maeparser is a Python library for reading and writing molecular data stored in Maestro files. It provides a simple interface for extracting structural information from Maestro files commonly used in molecular modeling and computational chemistry. | Python Library, Molecular Data, Maestro Files | Chemical Sciences | Library | Documentation, Uses, and more |
| mafft | ACES FASTER |
MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. It offers a range of algorithms and options for improving alignment quality. | Bioinformatics, Sequence Alignment, Phylogenetics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mageck | FASTER | MAGeCK is a computational model designed for the analysis of high-throughput CRISPR-Cas9 genetic screens to identify essential genes and pathways. | Crispr-Cas9, Genetic Screens, Essential Genes, Pathway Analysis | Genetics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| magic-blast | FASTER | Documentation, Uses, and more | ||||
| magics | ACES | Magics is a software library for visualizing meteorological data. It provides a wide range of graphical elements for the simultaneous representation of 2D and 3D data, including maps, wind fields, trajectories, symbols, etc. Magics is commonly used in weather forecasting, climate research, and meteorological data analysis. | Visualization, Meteorology, Meteorological Data, Weather Forecasting | Atmospheric Sciences, Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| magma | ACES Delta FASTER |
Magma is a software package designed for computations in algebra, number theory, algebraic geometry, and algebraic combinatorics. It provides a powerful tool for mathematical research and applications. | Mathematics, Algebra, Number Theory, Combinatorics | Algebra & Number Theory, Mathematics | Mathematical Software | Documentation, Uses, and more |
| mainmast | FASTER | MainMast is a software tool designed for high-throughput genetic data analysis, specifically focusing on Next-Generation Sequencing (NGS) data. It provides researchers with a user-friendly interface and a suite of analysis tools to efficiently process and interpret genetic data. | Ngs Analysis, Genetic Data Processing, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| make | ACES FASTER KyRIC |
Make is a build automation tool that automatically builds executable programs and libraries from source code by reading files called Makefiles which specifies how to derive the target program. | Build Automation, Software Development, Programming | Engineering & Technology | Utility | Documentation, Uses, and more |
| make_lastz_chains | FASTER | Documentation, Uses, and more | ||||
| makedepend | ACES FASTER |
makedepend is a tool used in software development to automatically generate dependencies of C source files. It is commonly used in projects utilizing makefiles to track dependencies and streamline the build process. | Software Development, Build Automation, Dependency Management | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| makeinfo | ACES FASTER |
makeinfo is a program that formats and prints Texinfo documentation. Texinfo is a typesetting syntax used for generating documentation in a variety of output formats such as HTML, DVI, PDF, PostScript, and plain text. | Documentation, Formatting, Texinfo, Build Systems | Other Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| mako | ACES FASTER |
Mako is a template library written in Python. It provides a familiar, non-XML syntax that compiles into Python modules for maximum performance. | Template Library, Python, Web Development | Computer & Information Sciences | Programming | Documentation, Uses, and more |
| mamba | ACES FASTER |
Mamba is a reimplementation of the high-performance package manager Conda that aims to be much faster in resolving package dependencies. It provides a simple and fast way to manage environments and packages for conda-enabled systems. | Package Manager, Dependency Resolver, Environment Management | Engineering & Technology | Package Manager | Documentation, Uses, and more |
| map | Stampede3 | Map is a software tool used for creating, visualizing, and analyzing geographical maps. It is commonly used in cartography and geographic information systems (GIS). | Mapping Software, Geographical Analysis, Cartography | Other Natural Sciences | Geospatial Software | Documentation, Uses, and more |
| margo | ACES | Documentation, Uses, and more | ||||
| mariadb | ACES FASTER |
MariaDB is a popular open source relational database management system (RDBMS) that is a drop-in replacement for MySQL. It is known for its high performance, scalability, and robust SQL support. MariaDB is developed by the original creators of MySQL and is designed for enterprise environments, web applications, and mission-critical systems. | Database Management System, Rdbms, Open Source, Sql | Computer & Information Sciences | Application Software | Documentation, Uses, and more |
| mariadb-connector-c | FASTER | Documentation, Uses, and more | ||||
| mash | ACES FASTER |
Mash is a fast and flexible genome distance estimator that can accurately estimate the pairwise genetic distance between genomes. It uses a MinHash dimensionality reduction technique to efficiently compute Jaccard distances between large sets of DNA sequences, enabling rapid genome comparisons. | Genome Distance Estimator, Minhash Technique, Jaccard Distances, DNA Sequences, Genome Comparisons | Biological Sciences | Documentation, Uses, and more | |
| mashmap | FASTER | mashmap is a reference-based approximate mapping tool designed for highly-divergent sequences. It efficiently aligns large genomes, offering flexibility and speed in detecting structural variations and similarities. | Mapping, Alignment, Genomics, Bioinformatics | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| masurca | FASTER | MaSuRCA (Maryland Super-Read Celera Assembler) is a hybrid and hierarchical genome assembler specifically designed for long reads like those produced by Pacific Biosciences or Oxford Nanopore Technologies. It aims to assemble genomes at high accuracy and contiguity using a combination of short Illumina reads and long error-prone reads. | Genome Assembly, Bioinformatics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| mathematica | FASTER Stampede3 |
Mathematica is a computational software program used in scientific, engineering, mathematical and computing fields. It provides a wide range of tools for symbolic and numerical computations, visualization, data analysis, and programming. | Computational Software, Mathematics, Data Analysis, Programming, Visualization | Applied Mathematics, Mathematics | Mathematical Software | Documentation, Uses, and more |
| matio | ACES | matio is a library for reading and writing MATLAB MAT files in C and Fortran. The library supports reading and writing Level 5 MAT files and supports most of the features of MAT 4 and MAT 5 MAT files. | Matlab Mat Files, C, Fortran | Other Mathematics, Mathematics | Data Management | Documentation, Uses, and more |
| matlab | ACES Anvil Bridges-2 Expanse FASTER Jetstream2 Ookami Stampede3 |
MATLAB is a high-performance language for technical computing and visualization. It integrates computation, visualization, and programming in an easy-to-use environment where problems and solutions are expressed in familiar mathematical notation. | Programming Language, Technical Computing, Visualization, Mathematical Notation | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| matlab-engine | FASTER | Documentation, Uses, and more | ||||
| matlab_unlicensed | Delta | Documentation, Uses, and more | ||||
| matlock | FASTER | Documentation, Uses, and more | ||||
| matplotlib | ACES FASTER |
Matplotlib is a comprehensive library for creating static, animated, and interactive visualizations in Python. It can be used to generate plots, histograms, power spectra, bar charts, error charts, scatterplots, etc. Matplotlib is highly customizable and offers a wide range of plotting options and styles. | Python Library, Data Visualization, Plotting Library | Computer & Information Sciences | Plotting & Graphing Tool | Documentation, Uses, and more |
| maturin | ACES FASTER |
Maturin is a Rust-native build system for Python packages that allows users to create wheels for their Python packages written in Rust. It aims to simplify the process of packaging and distributing Python extensions written in Rust, providing a seamless integration between Rust and Python ecosystems. | Python Packaging, Rust Programming Language, Build System, Python Extensions, Package Distribution | Computer & Information Sciences | Build System | Documentation, Uses, and more |
| mauve | FASTER | Mauve is a computational tool used for multiple genome alignment. It is specifically designed for aligning and analyzing genomes with an emphasis on rearrangements. | Computational Biology, Bioinformatics, Genome Alignment | Genomics, Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| maven | ACES FASTER |
Apache Maven is a build automation tool used primarily for Java projects. It manages project dependencies and provides a standardized way to build, test, and deploy Java software projects. | Build Automation, Dependency Management, Java Projects | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| maxbin | FASTER | Documentation, Uses, and more | ||||
| mbuffer | FASTER | mbuffer is a tool for buffering data streams that offers high-speed I/O performance and better throughput. It provides an efficient way to read and write data to and from various sources while optimizing the data transfer rate. | Data Streams, Buffering, Data Transfer, Optimization | Computer & Information Sciences | Documentation, Uses, and more | |
| mc | Bridges-2 | MC is a popular C compiler and interpreter that is widely used for developing efficient and portable software. | Compiler, Interpreter, C, Software Development | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| mccortex | FASTER | Mccortex is a software tool for assembling genomes quickly and efficiently by leveraging the compacted de Bruijn graph data structure. | Genomics, Bioinformatics, Computational Biology, Sequence Analysis | Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| mcl | FASTER | MCL (Markov Cluster Algorithm) is a clustering algorithm based on simulation of stochastic flow in graphs. It is commonly used for clustering network data to identify modules or communities of nodes with related functions or properties. | Clustering, Network Analysis, Graph Algorithms | Computer & Information Sciences | Clustering Algorithm | Documentation, Uses, and more |
| mcoutbryk | FASTER | mcoutbryk is a simulation software designed for Monte Carlo simulations in the field of computational chemistry. It aims to provide researchers and scientists with a tool for performing accurate and efficient simulations of chemical systems using Monte Carlo methods. | Monte Carlo Simulations, Computational Chemistry, Simulation Software | Physical Sciences, Other Natural Sciences | Research Tool | Documentation, Uses, and more |
| mcscanx | FASTER | MCScanX is a toolkit specifically designed for detecting collinear gene pairs within multiple genomes or subgenomes and inferring the syntenic relationships among them. It allows for the analysis of gene synteny and evolutionary relationships, aiding in understanding gene duplication and divergence events. | Gene Synteny, Genomic Analysis, Syntenic Relationships | Biological Sciences | Tool | Documentation, Uses, and more |
| mctc-lib | FASTER | Documentation, Uses, and more | ||||
| mdanalysis | FASTER | Documentation, Uses, and more | ||||
| mdi | ACES FASTER |
Documentation, Uses, and more | ||||
| mdspan | Stampede3 | mdspan is a C++ library that provides a multidimensional array data structure with a fixed size at compile time. It offers a high-performance alternative to traditional dynamically allocated multidimensional arrays. | C++ Library, Multidimensional Array, Data Structure, High-Performance Computing | Computer & Information Sciences | Data Structure | Documentation, Uses, and more |
| mdtest | Delta | MDTest is a file system metadata benchmark that includes tests to measure metadata operations, such as file creates, stat operations, and directory operations. It is often used to assess the metadata performance of parallel file systems. | Benchmarking, File System, Metadata | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mdtraj | ACES | Documentation, Uses, and more | ||||
| medaka | FASTER | Medaka is a tool for nanopore consensus sequence calling in real-time. It is designed to provide a high-accuracy consensus sequence for a given set of nanopore reads. | Bioinformatics, Ngs Data Analysis, Nanopore Sequencing, Consensus Sequence Calling | Biological Sciences | Ngs Data Analysis Tool | Documentation, Uses, and more |
| meep | Anvil | Meep (or MIT Electromagnetic Equation Propagation) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. | Simulation, Electromagnetics, Fdtd | Physical Sciences | Computational Software | Documentation, Uses, and more |
| mef90 | FASTER | Documentation, Uses, and more | ||||
| mega | FASTER | Documentation, Uses, and more | ||||
| megahit | FASTER | MEGAHIT is a highly efficient and ultra-fast single-nucleotide polymorphism (SNP)-aware metagenome assembly software tool. It is designed for the assembly of metagenomic sequencing data, providing users with high-quality draft assemblies. | Metagenome Assembly, Bioinformatics, Sequencing Data, Snp-Aware, Draft Assemblies | Bioinformatics, Biological Sciences | Assembly Software | Documentation, Uses, and more |
| megan | FASTER | MEGAN (MEtaGenome ANalyzer) is a comprehensive software package for analyzing large metagenomic data sets. It is designed to facilitate the exploration and taxonomic analysis of complex microbiomes. | Metagenomics, Microbiome, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| meme suite | Bridges-2 | Documentation, Uses, and more | ||||
| memoryviewer | ACES | MemoryViewer is a software tool used for analyzing and visualizing memory usage and data structures within computer programs. It allows users to track memory allocation, deallocation, and usage patterns to optimize memory management. | Memory Management, Software Development, Performance Analysis | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| mentorgraphics | Bridges-2 | The MentorGraphics/tessent.2022.1 modulefile provides Mentor Graphics Tessent 2022.1. Design augmentation and linked applications that detect, mitigate and eliminate risks throughout the IC lifecycle, helping customers address their debug, test, yield, safety, security, and optimization requirements for today’s most complex SoCs. | Documentation, Uses, and more | |||
| mercurial | ACES Ookami |
Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an intuitive interface. | Version Control, Software Development | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| mercury | ACES | Documentation, Uses, and more | ||||
| mesa | ACES FASTER |
Mesa is an open-source agent-based modeling framework that allows users to create and analyze computational models of complex adaptive systems. | Agent-Based Modeling, Complex Systems, Simulation, Computational Modeling | Other Computer & Information Sciences, Computer & Information Sciences | Framework | Documentation, Uses, and more |
| mesa-glu | Anvil | mesa-gl is an open-source implementation of the OpenGL specification, a system for rendering interactive 3D graphics, and a widely used and versatile graphics library. mesa-glu is the OpenGL Utility Library (GLU) component of Mesa, providing useful functions for building OpenGL applications. | Graphics, 3D Graphics, Opengl, Graphics Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| meson | ACES Delta DeltaAI FASTER |
Meson is an open-source build system meant to be both extremely fast and as user-friendly as possible. | Build System, Software Development, Automation | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| meson-python | ACES FASTER |
Meson is a high-productivity build system. It provides a simple syntax for describing how your project is build and a wide range of options to control the build process. | Build System, Automation, Software Development | Computer & Information Sciences | Build System | Documentation, Uses, and more |
| metabat | FASTER | MetaBAT is a software tool for reconstructing single genomes from complex microbial communities for metagenomics analysis. It utilizes a mixture model to leverage the differential abundance of unique sequences to bin contigs according to their species origin. | Metagenomics, Microbial Communities, Genome Reconstruction | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| metadecoder | FASTER | Documentation, Uses, and more | ||||
| metaeuk | ACES FASTER |
Documentation, Uses, and more | ||||
| metagenomics | Ookami | Documentation, Uses, and more | ||||
| metaphlan | ACES FASTER |
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes to identify and quantify the presence of microbial species in a sample. | Metagenomics, Microbiome, Microbial Ecology, Bioinformatics | Environmental Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| methylpy | Bridges-2 | methylpy is a Python package designed for the analysis of DNA methylation data obtained from bisulfite sequencing. It provides various tools for processing, analyzing, visualizing, and interpreting DNA methylation data. | DNA Methylation, Bisulfite Sequencing, Epigenetics, Bioinformatics, Python Package | Genetics, Biological Sciences | Python Library | Documentation, Uses, and more |
| metis | ACES Delta FASTER Stampede3 |
Metis is a computational software library for partitioning graphs, meshes, and hypergraphs. It provides algorithms that can efficiently partition large graphs and meshes while minimizing the edge-cuts and balancing the partition sizes. | Computational Software, Graph Partitioning, Mesh Partitioning, Hypergraph Partitioning | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| mfem | ACES FASTER Stampede3 |
MFEM is a lightweight, general, scalable C++ library for finite element methods. Its features include a wide range of finite element spaces, high-order and variable-order discretizations, parallel computing support, and multiple examples and applications. | Finite Element Method, C++ Library, Parallel Computing | Engineering & Technology | Library | Documentation, Uses, and more |
| mgard | ACES | Documentation, Uses, and more | ||||
| mgltools | FASTER | Documentation, Uses, and more | ||||
| micro-c | FASTER | Documentation, Uses, and more | ||||
| micromamba | ACES FASTER |
Documentation, Uses, and more | ||||
| minialign | Bridges-2 | minialign is an ultrafast, memory efficient, and highly accurate tool for multiple sequence alignment (MSA) of biological sequences. It is designed to handle very large datasets with high throughput. The software employs a k-mer based approach for rapid pairwise alignment followed by progressive alignment to generate the final MSA. | Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| miniasm | FASTER | Miniasm is a minimal-contig assembler that generates long noisy read assemblies using the Overlap-Layout-Consensus (OLC) paradigm. | Assembly, Genome, Sequence Analysis | Biological Sciences | Assembler | Documentation, Uses, and more |
| miniconda cuquantum | DeltaAI | Documentation, Uses, and more | ||||
| miniconda3 | ACES FASTER KyRIC |
Miniconda is a free minimal installer for conda. It is a package management system that simplifies the installation and management of software packages. Miniconda allows users to create environments containing dependencies from a specified list of packages, making it easier to manage different projects with conflicting package requirements. | Package Management, Dependency Management, Software Installation | Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| miniforge3 | ACES FASTER |
Documentation, Uses, and more | ||||
| minigraph | FASTER | Documentation, Uses, and more | ||||
| minimap2 | ACES FASTER |
Minimap2 is a versatile sequence alignment program that can be used for mapping DNA or cDNA sequences to a reference genome. It is known for its speed and accuracy, making it a popular choice for various bioinformatics applications. | Sequence Alignment, Bioinformatics, Genomics, Computational Biology | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| miniprot | FASTER | Miniprot is a software tool for predicting and modeling protein structures, including protein folding, structure prediction, and structural analysis. It is designed to be user-friendly and efficient for researchers working in the field of protein structure prediction and molecular modeling. | Protein Structure Prediction, Molecular Modeling, Protein Folding, Structural Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Prediction & Modeling | Documentation, Uses, and more |
| minizip | ACES FASTER |
Minizip is a minimalistic, open-source library that provides a simple API to create, read, and update zip files. It is a lightweight solution for working with zip archives in C or C++ projects. | Compression, Archiving, Library, Open Source | Compression/Archiving | Documentation, Uses, and more | |
| minpath | ACES FASTER |
Documentation, Uses, and more | ||||
| mkfontdir | DeltaAI | Documentation, Uses, and more | ||||
| mkfontscale | DeltaAI | Documentation, Uses, and more | ||||
| mkl | KyRIC | Intel Math Kernel Library (Intel MKL) is a highly optimized, thread-safe, mathematical library for performing mathematical, statistical, and data analysis computations. It offers high-performance implementations of BLAS, LAPACK, ScaLAPACK, sparse solvers, FFT, and more for Intel processors. | Mathematical Library, Optimized Computations, Thread-Safe Functions | Applied Mathematics, Mathematics | Computational Software | Documentation, Uses, and more |
| mkl-service | FASTER | mkl-service is part of the Intel Math Kernel Library (MKL) that provides optimized performance for mathematical, scientific, and engineering computations on Intel architectures. It provides a set of routines optimized for use with Intel processors. | Mathematics, Computer Science, Software Engineering, Systems & Development | Computer & Information Sciences | Mathematical Computing | Documentation, Uses, and more |
| mkl32 | KyRIC | Intel(R) Math Kernel Library for 32-bit applications | Mathematics, Computational Software, Hpc Tools | Other Mathematics | Library | Documentation, Uses, and more |
| mkmod | Stampede3 | Documentation, Uses, and more | ||||
| ml-collections | ACES FASTER |
Documentation, Uses, and more | ||||
| ml_dtypes | ACES FASTER |
Documentation, Uses, and more | ||||
| mlflow | Bridges-2 FASTER |
MLflow is an open-source platform for managing the end-to-end machine learning lifecycle. It enables tracking experimentation, packaging code into reproducible runs, and sharing and deploying models. | Machine Learning, Data Science, Model Management, Experimentation, Model Deployment | Computer Science, Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| mlst | FASTER | Multi-Locus Sequence Typing (MLST) is a molecular typing method that characterizes isolates by sequencing a set of housekeeping genes. MLST is widely used in microbial genotyping studies to investigate the genetic relationships between isolates and is particularly popular in epidemiological and population biology studies. | Bioinformatics, Microbiology, Genotyping, Epidemiology, Population Biology | Microbial Genomics, Biological Sciences | Sequence Typing Tool | Documentation, Uses, and more |
| mlst_check | FASTER | Documentation, Uses, and more | ||||
| mm-common | FASTER | Documentation, Uses, and more | ||||
| mm2-plus | FASTER | Documentation, Uses, and more | ||||
| mmg | FASTER | Documentation, Uses, and more | ||||
| mmseqs2 | ACES FASTER |
MMseqs2 is a software suite for fast and sensitive sequence searching. It enables ultra-fast and sensitive sequence search and clustering functionality using a versatile and memory-efficient index data structure. | Sequence Searching, Sequence Clustering, Bioinformatics, Computational Biology | Biological Sciences | Sequence Search & Clustering Tool | Documentation, Uses, and more |
| moab | ACES FASTER |
Documentation, Uses, and more | ||||
| modeltest-ng | FASTER | ModelTest-NG is a software for the selection of nucleotide substitution models in phylogenetics. It uses model selection strategies to automatically choose the best-fit nucleotide substitution model for a given dataset, which is essential for accurate phylogenetic inference. | Phylogenetics, Model Selection, Phylogenetic Inference, Nucleotide Substitution Models | Bioinformatics, Biological Sciences | Model Selection Tool | Documentation, Uses, and more |
| modtree | Anvil | ModTree is a software tool for the reconstruction of modular trees of mRNA transcripts and alternative splicing events. It is designed to identify and visualize the modular organization of alternative splicing events within a transcriptome. | Transcriptomics, Alternative Splicing, Modular Trees, Data Analysis | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| modular | ACES | Documentation, Uses, and more | ||||
| module-git | Expanse Ookami |
module-git is a version control system designed to efficiently handle large projects, providing powerful branching, merging, and collaboration features. It allows multiple developers to work on the same codebase concurrently and maintain a complete history of changes. | Version Control, Distributed Version Control, Collaboration, Software Development | Documentation, Uses, and more | ||
| module-info | Expanse Ookami |
module-info is a software tool that provides information about loaded modules and their dependencies in a computing environment. It helps users to manage and troubleshoot software dependencies and configurations. | Software, Dependency Management, Software Configuration | Computer & Information Sciences | System Information Tool | Documentation, Uses, and more |
| moe | FASTER | MOE (Molecular Operating Environment) is a comprehensive molecular modeling and simulation software that provides tools for molecular visualization, protein modeling, docking, QSAR analysis, and more. | Molecular Modeling, Molecular Simulation, Protein Modeling, Docking, Quantum Mechanics, Pharmacophore Modeling | Bioinformatics, Biological Sciences | Analysis & Visualization Tool | Documentation, Uses, and more |
| mold | ACES FASTER |
Mold is a computational software tool developed for conducting molecular dynamics simulations in the field of biophysics and computational chemistry. It is designed to model the behavior of biomolecules and study their interactions at the atomic level. | Computational Software, Molecular Dynamics, Biophysics, Chemistry | Biophysics, Biological Sciences | Molecular Dynamics Simulator | Documentation, Uses, and more |
| molden | FASTER | Molden is a molecular visualization program specifically designed for the display and analysis of molecular structures. It provides various tools for visualizing molecular orbitals, electron densities, and other properties of chemical systems. | Molecular Visualization, Chemistry, Molecular Modeling | Physical Chemistry, Chemical Sciences | Molecular Visualization Tool | Documentation, Uses, and more |
| molmod | FASTER | MolMod is a versatile python library designed for molecular modeling and simulation. It provides a wide range of tools and functionalities for molecular dynamics simulations, quantum chemistry calculations, and biomolecular analysis. | Molecular Modeling, Simulation, Python Library, Quantum Chemistry, Biomolecular Analysis | Biological Sciences, Natural Sciences | Library | Documentation, Uses, and more |
| monai | ACES | MONAI (Medical Open Network for AI) is a PyTorch-based, open-source framework for healthcare imaging. It provides domain-optimized foundational capabilities for developing medical imaging deep learning algorithms. MONAI enables the reproducible and scalable research for the development of novel imaging technologies and clinical applications. | Deep Learning, Medical Imaging, Pytorch, Open Source | Biomedical Engineering, Engineering & Technology | Research | Documentation, Uses, and more |
| monitor | Anvil | A monitor is an electronic visual display for computers. It usually consists of a screen, circuitry, and casing. The display device in modern monitors is typically a thin film transistor liquid crystal display (TFT-LCD) or a flat panel LED display, while older monitors used a cathode ray tube (CRT). Monitors are used to display output from the computer's graphics card, allowing users to interact with the computer and its software. | Technology, Display, Computer Hardware | Device | Documentation, Uses, and more | |
| moose | FASTER | MOOSE (Multiphysics Object-Oriented Simulation Environment) is a finite element simulation framework designed for solving complex multiphysics and multiscale engineering problems. It provides a flexible and extensible platform for researchers and engineers to develop and deploy simulation tools for a wide range of applications. | Simulation, Multiphysics, Finite Element Method | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| mothur | FASTER | Mothur is a software package for bioinformatics analysis of microbial communities. It provides a suite of tools for processing high-throughput sequencing data, including quality control, alignment, taxonomy assignment, and diversity analysis. | Bioinformatics, Microbial Communities, High-Throughput Sequencing | Microbial Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| motif | ACES FASTER |
Motif is a software tool used for motif discovery and motif analysis in biological sequences. It is commonly employed in bioinformatics and computational biology to identify conserved patterns or motifs within nucleotide or protein sequences. | Bioinformatics, Computational Biology, Sequence Analysis | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| motioncor2 | FASTER | Documentation, Uses, and more | ||||
| mpc | ACES Anvil DeltaAI FASTER KyRIC |
MPC, short for Multi-Party Computation, is a cryptographic protocol that allows multiple parties to jointly compute a function over their inputs while keeping those inputs private. It ensures data privacy and security in collaborative computations. | Cryptographic Protocol, Secure Computation, Privacy-Preserving, Collaborative Computation | Computer & Information Sciences | Cryptographic Protocol | Documentation, Uses, and more |
| mpfr | ACES Anvil DeltaAI Expanse FASTER KyRIC Stampede3 |
The GNU MPFR (Multiple Precision Floating-Point Reliable) library is a C library for arbitrary-precision arithmetic on floating-point numbers that guarantees correctly rounded results. | Arbitrary-Precision Arithmetic, Floating-Point Computation, Mathematical Library | Mathematics | Computational Software | Documentation, Uses, and more |
| mpi | KyRIC | Message Passing Interface (MPI) is a standardized and portable message-passing system designed to enable scalable, parallel computing on a wide variety of parallel computers. It is widely used in the field of high-performance computing (HPC) to develop parallel programs that can run efficiently on distributed memory architectures. | Hpc, Parallel Computing, Message Passing, Scalable Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpi4py | ACES FASTER Ookami |
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language. It allows Python programs to directly interact with MPI parallel computation functionalities. | Parallel Computing, Message Passing Interface, Python Library | Computer & Information Sciences, Other Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| mpich | ACES DeltaAI FASTER KyRIC Ookami |
MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard. It enables parallel computing on a wide variety of platforms and architectures. | Mpi Implementation, Parallel Computing, High Performance Computing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| mpich-abi | DeltaAI | Documentation, Uses, and more | ||||
| mpifileutils | FASTER | Documentation, Uses, and more | ||||
| mpip | Delta DeltaAI |
mpip is a small utility that helps to install and manage MPI libraries on HPC clusters by simplifying the process of downloading, configuring, building, and installing MPI libraries. | Software Utility, Hpc, Mpi Libraries, Cluster Management, Installation Tool | Engineering & Technology | Documentation, Uses, and more | |
| mpixlate | DeltaAI | Documentation, Uses, and more | ||||
| mpl | Stampede3 | Documentation, Uses, and more | ||||
| mpmath | FASTER | Documentation, Uses, and more | ||||
| mrbayes | Anvil | MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. It employs Markov chain Monte Carlo methods to estimate the posterior distribution of model parameters. | Bayesian Inference, Phylogenetics, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Software Tool | Documentation, Uses, and more |
| mrcfile | ACES FASTER |
Documentation, Uses, and more | ||||
| mrnet | Delta DeltaAI |
MRNET (Mendelian Randomization using Network models) is a software package for performing causal inference through Mendelian randomization and network modeling. It allows researchers to investigate causal relationships between traits by leveraging genetic instrumental variables and network structures. | Causal Inference, Mendelian Randomization, Network Modeling, Genetic Instrumental Variables | Genetics, Biological Sciences | Research Tool | Documentation, Uses, and more |
| msgpack-c | FASTER | Documentation, Uses, and more | ||||
| mstore | FASTER | Documentation, Uses, and more | ||||
| mujoco | ACES FASTER |
MuJoCo is a physics engine for detailed, efficient and accurate simulation of complex dynamical systems. It is designed for high-fidelity modeling and simulation of computational and robotic systems in various domains. | Physics Engine, Simulation, Robotics | Artificial Intelligence & Intelligent Systems, Engineering & Technology | Physics Engine | Documentation, Uses, and more |
| mujoco-py | FASTER | mujoco-py is a Python library that provides a simplified interface to the MuJoCo physics engine for robotic simulations and control tasks. It allows users to create, manipulate, and control dynamic systems in a simulated environment. | Physics Engine, Robotic Simulations, Control Tasks, Simulation Environment | Computer Science, Engineering & Technology | Python Library | Documentation, Uses, and more |
| multicharge | FASTER | Documentation, Uses, and more | ||||
| multichoose | ACES FASTER |
multichoose is a Python library that implements the concept of multichoose, which calculates the number of ways to choose a certain number of items from a set where each item can be chosen multiple times. | Python Library, Combinatorics, Mathematics | Pure Mathematics, Mathematics | Mathematical Calculation Tool | Documentation, Uses, and more |
| multiqc | ACES FASTER |
MultiQC is a reporting tool that collects statistics from multiple bioinformatics analyses and generates a single report. It helps in summarizing the output from various bioinformatics tools in a standardized and consolidated format. | Bioinformatics, Computational Biology, Data Analysis, Reporting Tool | Biophysics, Biological Sciences | Visualization Tool | Documentation, Uses, and more |
| mummer | ACES FASTER |
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. It can also align a wide range of sequences, including protein-coding sequences. | Genome Alignment, Sequence Alignment, Bioinformatics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| mumps | ACES FASTER |
MUMPS (MUltifrontal Massively Parallel sparse direct Solver) is a software package for the parallel solution of large sparse systems of linear equations arising from computational science and engineering applications. | Linear Algebra, Sparse Matrices, Computational Science, Engineering | Applied Mathematics, Mathematics | Solver | Documentation, Uses, and more |
| muparser | Delta | muparser is a fast mathematical expression parser library written in C++. | Mathematical Expression Parser, Math Library, C++ Library | Other Mathematics | Mathematical Expression Parser | Documentation, Uses, and more |
| muscle | FASTER | MUSCLE (Multiple Sequence Comparison by Log-Expectation) is a software package for multiple sequence alignment. It offers high accuracy and speed, making it a popular choice for aligning large datasets of biological sequences. | Sequence Alignment, Bioinformatics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| musl | ACES | musl is a lightweight, fast, simple, and secure C library that targets modern Unix systems. It is designed for embedded systems, performance-critical applications, and other resource-constrained environments where a small footprint is essential. | C Library, Embedded Systems, Performance Optimization, Resource-Constrained Environments | Computer & Information Sciences | C Library | Documentation, Uses, and more |
| must | Bridges-2 | MuST is software package designed for performing ab initio electornic structure calculations for metals, alloys, and nanostructures. It is an all-electron DFT code based on multiple scattering theory, also known as KKR method, and Green function techniques. | Documentation, Uses, and more | |||
| mvapich | Delta Ookami Stampede3 |
MVAPICH (MPI for MVAPICH2) is an open-source MPI implementation that delivers high performance, scalability, and fault tolerance for parallel computing on large HPC systems. It is specifically designed for InfiniBand and Omni-Path architectures. | Hpc, Mpi, Parallel Computing, High Performance Computing | Engineering & Technology | Parallel Computing | Documentation, Uses, and more |
| mvapich-plus | ACES | Documentation, Uses, and more | ||||
| mvapich-plus-cpu | Stampede3 | Documentation, Uses, and more | ||||
| mvapich-plus-pvc | Stampede3 | Documentation, Uses, and more | ||||
| mvapich2 | Anvil Bridges-2 FASTER KyRIC Ookami |
MVAPICH2 is an open-source MPI implementation for InfiniBand, iWARP, and RoCE communication protocols which delivers high performance and scalability on a wide variety of HPC systems. | Mpi Implementation, High Performance Computing, Infiniband, Open-Source | Physical Sciences | Library/Tool | Documentation, Uses, and more |
| mvapich2-gdr | ACES | MVAPICH2-GDR is a high-performance MPI library designed for NVIDIA GPU Direct RDMA technology, allowing direct data transfers between GPUs and networking adapters without involving the CPU. It is optimized for HPC clusters and large-scale computing environments to achieve low latency and high message rate communication. | Hpc, Mpi Library, Gpu Direct Rdma, High-Performance Computing | Engineering & Technology | Library | Documentation, Uses, and more |
| mygene | ACES | Documentation, Uses, and more | ||||
| namd | ACES Anvil Bridges-2 Delta FASTER Ookami Stampede3 |
NAMD (NAnoscale Molecular Dynamics) is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is optimized for the simulation of biomolecular systems containing millions of atoms. | Molecular Dynamics, Biomolecular Systems, Parallel Computing, Cuda, Simulation | Biophysics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| namd-linux-x86_64-multicore | KyRIC | Documentation, Uses, and more | ||||
| namd-multicore-cuda | ACES | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Documentation, Uses, and more | |||
| namd-netlrts-smp-cuda | ACES | NAMD (NAnoscale Molecular Dynamics) is a high-performance molecular dynamics software that simulates large biomolecular systems. This version of NAMD is customized for parallel computing on multicore machines with CUDA support for GPU acceleration. | Molecular Dynamics, Simulation, Biomolecular Systems, Parallel Computing, Cuda, Gpu Acceleration | Bioinformatics, Biological Sciences | Scientific Software | Documentation, Uses, and more |
| namd-verbs-smp-cuda | ACES | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | Documentation, Uses, and more | |||
| namd3 | Delta | NAMD3 is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. It is capable of running on a wide range of hardware platforms, from individual workstations to large HPC clusters, making it suitable for a variety of research applications in biophysics and computational biology. | Molecular Dynamics, Biomolecular Systems, Computational Biology, Hpc, Parallel Computing | Biophysics, Biological Sciences | Scientific Simulation Software | Documentation, Uses, and more |
| namfinder | FASTER | Documentation, Uses, and more | ||||
| nano | ACES DeltaAI |
Documentation, Uses, and more | ||||
| nanofilt | FASTER | Nanofilt is a tool for filtering and trimming Oxford Nanopore sequencing data. It is specifically designed to process raw Nanopore reads and perform quality control operations to improve the accuracy and reliability of downstream analyses. | Bioinformatics, Sequence Analysis, Nanopore Sequencing | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| nanoflann | FASTER | Documentation, Uses, and more | ||||
| nanoget | ACES FASTER |
Documentation, Uses, and more | ||||
| nanomath | ACES FASTER |
Documentation, Uses, and more | ||||
| nanoplot | Bridges-2 | NanoPlot is a plotting tool specifically designed for visualization of long read sequencing data generated by Nanopore sequencers like MinION. It can create quality control plots to help users assess the quality and characteristics of the sequencing data. | Bioinformatics, Genomics, Sequencing Data, Quality Control, Visualization | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| napari | FASTER | Documentation, Uses, and more | ||||
| nasm | ACES DeltaAI FASTER |
NASM (Netwide Assembler) is an 80x86 and x86-64 assembler designed for portability and modularity. It supports a range of object file formats, including Linux and Windows executables, and generates code compatible with Intel syntax. | Assembler, Cross-Platform, X86, Programming | Computer Science, Computer & Information Sciences | Assembler | Documentation, Uses, and more |
| nbclassic | ACES FASTER |
Documentation, Uses, and more | ||||
| nbo | Expanse | Natural Bond Orbital (NBO) analysis is a popular method for understanding chemical bonding in molecules. It provides insight into the nature of chemical bonds, bond strengths, and electron delocalization. | Chemistry, Molecular Biology, Computational Chemistry | Physical Chemistry, Chemical Sciences | Molecular Modeling | Documentation, Uses, and more |
| ncbi-vdb | ACES FASTER |
NCBI-vdb is a collection of software tools for managing data from the NCBI Sequence Read Archive, the GenBank flatfile sequence databases, as well as a framework for loading data into third-party caller software. It provides tools for downloading, validating, transforming, and analyzing biological sequence data. | Bioinformatics, Sequence Data Management, Data Analysis | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| nccl | ACES Anvil Delta DeltaAI FASTER |
NCCL (NVIDIA Collective Communication Library) is a library of multi-GPU collective communication primitives that are topology-aware and can be used to implement collective communications algorithms within CUDA kernels. | Cuda, Parallel Computing, Multi-Gpu Communication, Gpu Programming, Hpc | Computer & Information Sciences | Parallel Computing | Documentation, Uses, and more |
| nccl-tests | FASTER | NVIDIA Collective Communications Library (NCCL) provides multi-GPU and multi-node collective communication primitives optimized for NVIDIA GPUs. nccl-tests is a collection of test utilities and benchmarks for NCCL. | Gpu, Collective Communication, Benchmarking, Performance Testing | Computer & Information Sciences | Testing & Benchmarking | Documentation, Uses, and more |
| ncdf4 | FASTER | Documentation, Uses, and more | ||||
| ncdu | Bridges-2 FASTER Ookami |
ncdu (NCurses Disk Usage) is a disk utility for analyzing disk usage in a terminal environment. It provides a fast way to see what directories are using the most space on a filesystem. | Disk Utility, Disk Usage Analyzer, Terminal Tool, Storage Management | Other Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| ncftp | Delta | ncftp is a powerful and easy-to-use command-line FTP client for various operating systems. It provides a wide range of features for transferring files over FTP protocols. | Ftp Client, Command-Line Interface, File Transfer, Automation | Other Natural Sciences | Client | Documentation, Uses, and more |
| ncl | ACES Anvil FASTER |
The NCAR Command Language (NCL) is a scripting language designed specifically for the analysis and visualization of scientific data. It is widely used in the atmospheric and related sciences. | Scientific Data Analysis, Data Visualization, Atmospheric Sciences | Environmental Sciences, Earth & Environmental Sciences | Scripting Language | Documentation, Uses, and more |
| nclncarg | Stampede3 | Documentation, Uses, and more | ||||
| nco | ACES Anvil Delta FASTER Stampede3 |
NCO (NetCDF Operators) is a suite of programs designed to help manipulate and analyze netCDF and HDF4 files. It provides a range of powerful tools for processing and analyzing climate and weather data stored in netCDF format. | Data Manipulation, Data Analysis, Climate Data, Netcdf, Hdf4 | Earth & Environmental Sciences | Documentation, Uses, and more | |
| ncurses | ACES Anvil Delta DeltaAI FASTER KyRIC Ookami |
ncurses is a programming library providing an API that allows the programmer to write text-based user interfaces on a terminal. | Programming Library, Text-Based User Interfaces, Terminal Applications | Computer Science, Computer & Information Sciences | Programming/Development | Documentation, Uses, and more |
| ncview | Anvil Bridges-2 FASTER Stampede3 |
ncview is a visual browser for netCDF format files used for earth system data. It provides functionalities for viewing, analyzing, and interacting with data stored in netCDF files. | Data Visualization, Netcdf, Earth System Data | Earth & Environmental Sciences | Data Analysis Tool | Documentation, Uses, and more |
| ndiff | Delta | ndiff is a command-line tool for comparing two Nmap XML output files. It parses the XML files and identifies the differences in the scan results, including changes in host status, open ports, service versions, and other scan details. | Network Security, Network Monitoring, Penetration Testing, Cybersecurity | Computer & Information Sciences | Security Tools | Documentation, Uses, and more |
| nedit | ACES FASTER |
Documentation, Uses, and more | ||||
| neovim | Delta | Documentation, Uses, and more | ||||
| neper | FASTER | Documentation, Uses, and more | ||||
| netcdf | ACES FASTER Ookami Stampede3 |
NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Scientific Data, Data Storage, Data Access, Data Formats, Data Manipulation, Data Visualization | Other Natural Sciences | Library | Documentation, Uses, and more |
| netcdf-c | Anvil Delta |
NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Data Format, Scientific Data, Data Access, Data Sharing | Other Natural Sciences | Data Format | Documentation, Uses, and more |
| netcdf-c++4 | ACES FASTER |
netCDF-C++4 is a C++ interface for netCDF4, which is a software library and file format for storing multidimensional scientific data. It provides an object-oriented programming interface to the netCDF library, allowing users to read and write data stored in netCDF format using C++. | Netcdf, C++ Interface, Scientific Data Storage | Other Natural Sciences | Data Storage | Documentation, Uses, and more |
| netcdf-combined | FASTER | NetCDF-COMBINED is a package that combines multiple NetCDF files together to create a single output file. It is specifically designed for manipulating large datasets stored in the NetCDF format. | Data Manipulation, Netcdf Files, Large Datasets, File Organization | Other Natural Sciences | Utility | Documentation, Uses, and more |
| netcdf-cxx4 | Anvil | netcdf-cxx4 is a C++ library for accessing netCDF-4 classic and extended model data formats. It provides a high-level interface for reading and writing netCDF-4 data files in C++. | Netcdf, C++, Data Format | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| netcdf-fortran | ACES Anvil Delta FASTER |
NetCDF-Fortran is a set of Fortran interfaces to the NetCDF library providing an easy-to-use, high-level access to the NetCDF file format for storing and sharing scientific data. | Scientific Data, Fortran Interface, Netcdf Library | Other Natural Sciences | Programming Interface | Documentation, Uses, and more |
| netcdf/gcc/64/gcc/64 | Expanse | Documentation, Uses, and more | ||||
| netcdf4-python | ACES FASTER |
NetCDF4 is a Python interface to the netCDF version 4 library. NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. | Python Library, Netcdf, Scientific Data Handling, Array-Oriented Data, Data Storage & Access | Earth & Environmental Sciences | Library | Documentation, Uses, and more |
| netlib-lapack | Anvil Delta |
Netlib LAPACK (Linear Algebra PACKage) is a widely-used library for numerical linear algebra. It provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. | Numerical Computing, Linear Algebra, Library, Numerical Analysis | Computer & Information Sciences | Library | Documentation, Uses, and more |
| netlib-scalapack | Delta | ScaLAPACK is a library of high-performance linear algebra routines for parallel distributed memory machines. ScaLAPACK solves dense and banded linear systems, least squares problems, eigenvalue problems, and singular value problems. Description Source: https://www.netlib.org/scalapack/ |
Documentation, Uses, and more | |||
| netperf | Expanse Ookami |
Documentation, Uses, and more | ||||
| nettle | ACES DeltaAI FASTER |
Nettle is a cryptographic library that is designed to be low-level and general-purpose, offering several cryptographic algorithms such as AES, ARCFOUR, Blowfish, and MD5. | Cryptography, Security, Library | Computer & Information Sciences, Computer Science | Library | Documentation, Uses, and more |
| networkx | ACES FASTER |
NetworkX is a Python package for the creation, manipulation, and study of complex networks or graphs. It provides data structures for representing many types of networks, algorithms for analyzing them, and visualization tools to display them. | Python Library, Graph Theory, Network Analysis, Data Visualization | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| neuromancer | FASTER | Documentation, Uses, and more | ||||
| newick_utils | FASTER | Newick Utils is a collection of command-line tools for processing Newick tree files used in phylogenetics and computational biology. It provides various utilities for manipulating, analyzing, and visualizing phylogenetic trees represented in the Newick format. | Phylogenetics, Bioinformatics, Computational Biology, Phylogenetic Trees, Command-Line Tools | Bioinformatics, Biological Sciences | Command-Line Utility | Documentation, Uses, and more |
| nextdenovo | FASTER | NextDenovo is a software tool designed for de novo transcriptome assembly from RNA-seq data. It leverages de Bruijn graphs and utilizes a hybrid approach combining both OLC (Overlap-Layout-Consensus) and DBG (De Bruijn Graph) strategies to efficiently reconstruct the transcriptome in the absence of a reference genome. | Bioinformatics, Transcriptome Assembly, De Novo Assembly | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| nextflow | ACES Anvil Bridges-2 FASTER |
Nextflow is a powerful workflow manager that enables the writing of parallel and scalable computational workflows using native, containerized, or cloud-enabled execution environments. | Workflow Manager, Computational Biology, Data Science | Biological Sciences | Open Source | Documentation, Uses, and more |
| nextpolish | FASTER | NextPolish is a versatile and efficient tool for correcting long reads generated by third-generation sequencing technologies. It uses a noise model and an expectation-maximization algorithm to polish raw reads, improving their accuracy for downstream analysis. | Bioinformatics, Computational Biology, Long-Read Sequencing, Error Correction | Genetics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| nf-core | Anvil | NF-core is a collection of community curated Nextflow pipelines available for genomics, transcriptomics, and other bioinformatics analyses. It provides a collection of best practices workflows that are highly optimized, scalable, and easy to use. | Bioinformatics, Workflow Management, Nextflow, Genomics, Transcriptomics | Bioinformatics, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| ngc | Anvil | NGC is a cloud-based hub that provides users with a comprehensive catalog of GPU-optimized software for deep learning, machine learning, and HPC applications. It offers a platform for easy deployment and integration of GPU-accelerated applications in various domains. | Cloud Computing, Deep Learning, Machine Learning, Hpc | Computer & Information Sciences | Platform | Documentation, Uses, and more |
| ngc/cuquantum-appliance | DeltaAI | Documentation, Uses, and more | ||||
| nghttp2 | ACES DeltaAI FASTER |
nghttp2 is an open-source implementation of the Hypertext Transfer Protocol version 2 (HTTP/2) and its header compression algorithm. The project also include a HTTP/2 server, client, and proxy. | Http/2, Web Protocol, Networking | Computer & Information Sciences | Library | Documentation, Uses, and more |
| nghttp3 | ACES FASTER |
nghttp3 is an implementation of HTTP/3 and QUIC protocol in C programming language. It provides a low-level API for developers to interact with HTTP/3 and QUIC connections. | Http/3, Quic, Networking, Protocol | Computer & Information Sciences | Protocol | Documentation, Uses, and more |
| ngs | FASTER | NGS (Next-Generation Sequencing) refers to high-throughput sequencing technologies that allow for rapid and cost-effective sequencing of DNA and RNA. NGS has revolutionized genomics research, enabling various applications in areas such as genetics, personalized medicine, and evolutionary biology. | Ngs, Next-Generation Sequencing, Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ngsadmix | FASTER | NGSadmix is a software tool used for analyzing genetic admixture, which is the result of mixing genetic material from different ancestral populations within a population or individual. It is specifically designed to estimate individual admixture proportions and infer the number of ancestral populations contributing to a target population. | Genetic Admixture, Population Genetics, Ancestral Populations, Genomics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ngtcp2 | ACES FASTER |
ngtcp2 is a C library implementation of the QUIC protocol (IETF draft) for building QUIC servers and clients. | Quic Protocol, C Library, Networking | Computer & Information Sciences | Library | Documentation, Uses, and more |
| nibabel | ACES | NiBabel is a Python library that provides read and write access to some common medical and neuroimaging file formats, including NIfTI-1, NIfTI-2, and Analyze. It aims to simplify the process of working with neuroimaging data in Python. | Python Library, Neuroimaging, Medical Imaging, File Format, Nifti | Biological Sciences | Imaging & Visualization | Documentation, Uses, and more |
| ninja | ACES Delta DeltaAI FASTER Ookami Stampede3 |
ninja is a small build system with a focus on speed. It differs from other build systems in that it is designed to have its input files generated by a higher-level build system (like CMake) and will not execute commands in parallel by default. | Build System, Software Development, Automation | Software Engineering, Systems & Development, Engineering & Technology | Utility | Documentation, Uses, and more |
| nlohmann_json | ACES FASTER |
nlohmann_json is a JSON library for modern C++. It provides a simple and efficient way to work with JSON data in C++ programs. | Json Library, C++ | Computer & Information Sciences | Data Handling | Documentation, Uses, and more |
| nlopt | ACES FASTER |
NLopt is an open-source library for nonlinear optimization problems. It provides a common interface for several different optimization algorithms, allowing users to easily switch between them. | Optimization, Library, Open-Source | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| nltk | ACES Anvil FASTER |
NLTK, or Natural Language Toolkit, is a leading platform for building Python programs to work with human language data. It provides easy-to-use interfaces to over 50 corpora and lexical resources such as WordNet, along with a suite of text processing libraries for classification, tokenization, stemming, tagging, parsing, and semantic reasoning. | Python Library, Text Processing, Natural Language Processing | Informatics, Analytics & Information Science, Computer & Information Sciences | Text Analysis | Documentation, Uses, and more |
| nmad | ACES | nMAD (normalized mean absolute deviation) is a measure of dispersion for a set of data points. It is used to quantify the variability or spread of the data. nMAD is calculated as the mean of the absolute differences between each data point and the mean of the data, divided by a constant factor for normalization. | Statistics, Data Analysis, Data Normalization | Other Mathematics | Measurement Tool | Documentation, Uses, and more |
| node | Delta | Node.js is an open-source, cross-platform JavaScript runtime environment that executes JavaScript code outside of a web browser. It allows developers to use JavaScript for server-side scripting and runs scripts server-side to produce dynamic web page content before returning this content to the client's web browser. | Javascript, Server-Side Scripting, Cross-Platform | Computer & Information Sciences | Programming Platform | Documentation, Uses, and more |
| nodejs | ACES FASTER |
Node.js® is an open-source, cross-platform JavaScript runtime environment. Description Source: https://nodejs.org/en |
Documentation, Uses, and more | |||
| nostack | Expanse | nostack is a platform that allows users to visually design and build custom web and mobile applications without writing code. It provides a visual interface for drag-and-drop creation of applications. | Visual Development, No-Code Platform, Application Design, Web Development | Engineering & Technology, Computer & Information Sciences | Development Platform | Documentation, Uses, and more |
| nosve | Ookami | Documentation, Uses, and more | ||||
| nseg | FASTER | Documentation, Uses, and more | ||||
| nspr | ACES FASTER |
nspr (Netscape Portable Runtime) provides a platform-neutral API for system level and libc-like functions. nspr is a platform abstraction library for C/C++. It provides many useful APIs for cross-platform development. | Platform-Abstraction, Cross-Platform, Api, System-Level Functions | Computer & Information Sciences | Documentation, Uses, and more | |
| nss | ACES FASTER |
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. It provides a complete open-source implementation of cryptographic libraries supporting Secure Sockets Layer (SSL) and Transport Layer Security (TLS) protocols. | Security, Network, Encryption | Computer & Information Sciences | Security | Documentation, Uses, and more |
| nsync | ACES FASTER |
Nsync is a command-line tool for synchronizing files and directories between two locations. It allows users to easily mirror data between local and remote locations, ensuring that the contents are up to date in both places. | File Synchronization, Data Mirroring, Command-Line Tool | Computer Science, Engineering & Technology | File Synchronization Tool | Documentation, Uses, and more |
| ntl | ACES | ntl is a high-performance, portable C++ library providing data types for arbitrary length integers and floating-point numbers. It aims to offer efficient implementations for the fundamental algorithms in number theory. | Arbitrary Length Integers, Number Theory, High-Performance Computing, C++ Library | Pure Mathematics, Mathematics | Data Types & Algorithms | Documentation, Uses, and more |
| ntlink | FASTER | Documentation, Uses, and more | ||||
| ntpoly | ACES FASTER |
Documentation, Uses, and more | ||||
| nuitka | FASTER | Nuitka is a Python compiler written in Python. It helps in compiling Python source code to C code, thereby making it possible to create standalone executable programs from Python scripts. | Python Compiler, Source Code Optimization, Executable Program Generation | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| numactl | ACES Anvil Expanse FASTER KyRIC |
Numactl is a set of tools that allows you to have more control over NUMA (Non-Uniform Memory Access) systems. It provides utilities for memory placement and migration of processes and controlling the NUMA policy of a process. | Numa, Memory Management, Performance Optimization | Other Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| numba | ACES FASTER |
Numba is an open-source just-in-time (JIT) compiler that translates a subset of Python and NumPy code into fast machine code. | Jit Compiler, Python Optimization, Numpy Optimization | Computer & Information Sciences | Open-Source | Documentation, Uses, and more |
| numexpr | FASTER | Numexpr is a fast numerical expression evaluator for NumPy. With it, expressions that operate on arrays (like '3*a+4*b') are accelerated and use less memory than doing the same calculation in Python. In addition, its multi-threaded capabilities can make use of all your cores in a CPU. | Numerical Computation, Numerical Expressions, Array Operations, Performance Optimization, Multi-Threading | Computer & Information Sciences | Numerical Computation | Documentation, Uses, and more |
| numpy | ACES | NumPy is a fundamental package for scientific computing with Python. It contains functionality for multidimensional arrays, high-level mathematical functions such as linear algebra operations, Fourier transformations, and random number generation. NumPy can be utilized to solve linear algebraic equations, perform statistical analysis, create software simulations, and much more. | Scientific Computing, Numerical Computing, Data Analysis, Mathematics | Computer & Information Sciences, Mathematics | Computational Software | Documentation, Uses, and more |
| nv-codec-headers | FASTER | NVIDIA Video Codec SDK includes software development kits, samples, and documentation for encoding, decoding, and transcoding video and audio content. It provides low-level APIs for enabling applications to utilize NVIDIA GPU hardware accelerated video processing capabilities. | Video Processing, Gpu Acceleration, Software Development Kit, Video Codec, Nvidia | Computer & Information Sciences | Library | Documentation, Uses, and more |
| nvbio | FASTER | nvbio is a GPU-accelerated library of high-performance bioinformatics algorithms designed to leverage the parallel processing power of NVIDIA GPUs. It offers various tools for DNA sequence analysis and manipulation, allowing for faster and more efficient processing of large-scale genomic data. | Bioinformatics, Gpu Acceleration, Genomic Data Processing, DNA Sequence Analysis | Biological Sciences | Library | Documentation, Uses, and more |
| nvcomp | FASTER | nvcomp is a CUDA library providing GPU-accelerated compression and decompression algorithms. It aims to provide fast and efficient data compression techniques for GPU computing. | Compression, Gpu-Accelerated, Cuda, Data Processing | Computer Science, Computer & Information Sciences | Compression | Documentation, Uses, and more |
| nvhpc | ACES Anvil Bridges-2 Delta DeltaAI FASTER Jetstream2 Ookami |
NVIDIA HPC SDK is a comprehensive, integrated suite of compilers, libraries, and tools for the development and optimization of GPU-accelerated high-performance computing (HPC) applications. | Hpc, Gpu Acceleration, Compilers, Libraries, Development Tools | Computer Science, Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| nvhpc-byo-compiler | Ookami | Documentation, Uses, and more | ||||
| nvhpc-hpcx | Ookami | Documentation, Uses, and more | ||||
| nvhpc-mixed | DeltaAI | Documentation, Uses, and more | ||||
| nvhpc-nompi | Ookami | Documentation, Uses, and more | ||||
| nvhpc-openmpi3 | Ookami | Documentation, Uses, and more | ||||
| nvhpc_latest | Delta | NVIDIA HPC SDK is a comprehensive suite of compilers, libraries, and tools for accelerating HPC applications on GPU-accelerated systems. | Hpc, Compiler, Math Library, Software Development | Engineering & Technology | Tool | Documentation, Uses, and more |
| nvidia | Delta DeltaAI |
NVIDIA Corporation is an American technology company that designs graphics processing units (GPUs) for the gaming, cryptocurrency, and professional markets, as well as system on a chip units (SoCs) for the mobile computing and automotive market. | Graphics Processing Units, High-Performance Computing, Deep Learning, Data Analytics | Computer & Information Sciences | Graphics Processing Units | Documentation, Uses, and more |
| nvidia compilers | Stampede3 | Documentation, Uses, and more | ||||
| nvidia cuda toolkit | Bridges-2 | Documentation, Uses, and more | ||||
| nvidia hpc sdk | Anvil | Documentation, Uses, and more | ||||
| nvidia-mixed | DeltaAI | Documentation, Uses, and more | ||||
| nvitop | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-blas | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-fft | DeltaAI | Documentation, Uses, and more | ||||
| nvpl-lapack | DeltaAI | Documentation, Uses, and more | ||||
| nvshmem | ACES FASTER |
nvshmem is a GPU-accelerated implementation of the OpenSHMEM standard designed for NVIDIA GPUs. It provides a high-performance, parallel programming model for developing applications on GPU clusters. | Gpu-Accelerated, Openshmem, Nvidia Gpus | Computer & Information Sciences, Other Computer & Information Sciences | Library | Documentation, Uses, and more |
| nvtop | ACES Delta FASTER |
nvtop is an NVIDIA GPU system monitoring tool with a user-friendly CLI interface. It provides real-time monitoring of GPU utilization, memory usage, temperature, power consumption, and other important metrics. | System Monitoring, Gpu Monitoring, Nvidia Gpu, Command-Line Interface, Performance Optimization | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| nwchem | Anvil Bridges-2 Delta Stampede3 |
NWChem is an open-source computational chemistry package designed for high-performance simulations of large-scale molecular systems. It provides various tools and algorithms for both classical and quantum chemical calculations. | Computational Chemistry, High-Performance Computing, Open-Source Software | Physical Chemistry, Chemical Sciences | Computational Chemistry Software | Documentation, Uses, and more |
| obitools3 | FASTER | Obitools3 is a comprehensive package for analyzing and processing metagenomic data. It includes a variety of tools for quality control, taxonomic assignment, and diversity analysis of DNA sequences obtained from environmental samples. | Metagenomics, Bioinformatics, Microbiome Analysis, High-Throughput Sequencing | Biological Sciences | Bioinformatics Software | Documentation, Uses, and more |
| ocaml | ACES | Documentation, Uses, and more | ||||
| oclfpga | KyRIC | oclfpga is an OpenCL framework for FPGA acceleration. It allows users to utilize the power of Field-Programmable Gate Arrays (FPGAs) for accelerating applications through OpenCL programming. | Opencl, Fpga, Acceleration | Engineering & Technology | Framework | Documentation, Uses, and more |
| octave | Anvil Bridges-2 FASTER Ookami |
Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems and has extensive graphics capabilities for data visualization and manipulation. | Numerical Computations, Data Visualization | Mathematics, Computer & Information Sciences | Numerical Computation Software | Documentation, Uses, and more |
| octopus | FASTER Stampede3 |
Documentation, Uses, and more | ||||
| octopus-vcf | FASTER | Documentation, Uses, and more | ||||
| ogdf | FASTER | OGDF (Open Graph Drawing Framework) is a C++ library for the automatic layout of diagrams and graphs. It provides a wide range of algorithms and data structures for various graph drawing tasks. | Graph Drawing, Layout Algorithms, C++ Library | Computer Science, Computer & Information Sciences | Graph Visualization | Documentation, Uses, and more |
| ohpc | KyRIC | OpenHPC is a collaborative, community-driven effort to provide a comprehensive and cohesive open-source HPC stack to the community. Through close collaboration with key stakeholders across the industry, OpenHPC aims to provide a reference collection of open-source HPC software components and best practices to enable the development, testing, and deployment of HPC systems. Ultimately, building on the resecarch outputs from various related fields. | Hpc, High Performance Computing, Open-Source, Collaborative, Community-Driven | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| oneapi | Anvil FASTER |
OneAPI is a unified programming model that aims to simplify development across diverse architectures such as CPUs, GPUs, FPGAs, and other accelerators. It provides a single programming interface for developers to efficiently target and deploy applications in heterogeneous computing environments. | Heterogeneous Computing, Unified Programming Model, Accelerated Computing, Performance Optimization | Computer & Information Sciences | Unified Programming Model | Documentation, Uses, and more |
| onnx | ACES Anvil FASTER |
ONNX (Open Neural Network Exchange) is an open-source format for AI models. It enables interoperability between different frameworks, making it easier to move models between various tools and platforms. | Ai, Machine Learning, Deep Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Interoperability Format | Documentation, Uses, and more |
| onnx-runtime | ACES FASTER |
ONNX Runtime inference can enable faster customer experiences and lower costs, supporting models from deep learning frameworks such as PyTorch and TensorFlow/Keras as well as classical machine learning libraries such as scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different hardware, drivers, and operating systems, and provides optimal performance by leveraging hardware accelerators where applicable alongside graph optimizations and transforms. | Documentation, Uses, and more | |||
| ont-fast5-api | FASTER | Documentation, Uses, and more | ||||
| ont-guppy | FASTER | Documentation, Uses, and more | ||||
| ont-guppy-cpu | FASTER | Documentation, Uses, and more | ||||
| oom-explain | Ookami | Documentation, Uses, and more | ||||
| opari2 | ACES | OPARI2 (OpenMP Parallelizer and Runtime Instrumentation) is a tool for the parallelization and instrumentation of OpenMP programs. It helps to analyze and optimize the performance of parallel codes that use OpenMP directives. | Parallelization, Performance Analysis, Openmp | Computer & Information Sciences | Compiler/Analyzer | Documentation, Uses, and more |
| open-data-cube-core | FASTER | Open Data Cube (ODC) is an open-source software package that helps in the management, analysis, and visualization of large environmental and Earth observation data sets. ODC Core provides the foundational components and functionalities for working with satellite and Earth observation data. | Earth Observation, Data Management, Data Analysis, Data Visualization, Open Source | Earth & Environmental Sciences | Software Library | Documentation, Uses, and more |
| openai-gym | FASTER | Documentation, Uses, and more | ||||
| openbabel | ACES FASTER |
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It’s an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Description Source: https://openbabel.org/ |
Documentation, Uses, and more | |||
| openblas | ACES Anvil Bridges-2 Delta DeltaAI FASTER KyRIC Ookami |
OpenBLAS is an open-source implementation of the Basic Linear Algebra Subprograms (BLAS) library with optimized functions for matrix operations and linear algebra computations. It provides fast and efficient routines for common linear algebra operations. | Linear Algebra, Blas Library, Optimized Functions, Open Source | Mathematics, Computer & Information Sciences | Documentation, Uses, and more | |
| openblas/dynamic | Expanse | Documentation, Uses, and more | ||||
| opencensus-python | FASTER | OpenCensus is a set of libraries for various programming languages that helps developers collect performance and tracing data from their applications. The opencensus-python library specifically provides support for Python applications to enable monitoring and distributed tracing. | Monitoring, Distributed Tracing, Performance, Python | Computer & Information Sciences | Application Development | Documentation, Uses, and more |
| opencilk | Stampede3 | Documentation, Uses, and more | ||||
| opencv | ACES Anvil Bridges-2 Delta FASTER |
OpenCV (Open Source Computer Vision Library) is an open-source computer vision and machine learning software library. It provides a wide range of functionalities for real-time computer vision, including image processing, object detection, object tracking, and machine learning algorithms. | Computer Vision, Image Processing, Machine Learning, Open Source | Computer Science, Computer & Information Sciences | Computer Vision Library | Documentation, Uses, and more |
| openexr | ACES FASTER |
OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic (ILM) for use in computer imaging applications. It is used for the interchange of high-fidelity image data between different software applications. | Image, File Format, High Dynamic-Range, Hdr, Image Data | Engineering & Technology | File Format | Documentation, Uses, and more |
| openfoam | ACES Anvil Bridges-2 FASTER Ookami Stampede3 |
OpenFOAM (Open Source Field Operation and Manipulation) is a free, open-source computational fluid dynamics (CFD) software package developed by the OpenFOAM Foundation. It is widely used for simulating complex fluid flows in various industries and academic research. | Computational Fluid Dynamics, Open-Source Software, Finite Volume Method, Hpc | Fluid Dynamics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| openfold | ACES FASTER |
openfold is a computational software tool designed for protein folding simulations and structural analysis. It allows researchers to study the folding pathways of proteins and investigate their three-dimensional structures. | Computational Software, Molecular Dynamics Simulations, Protein Folding, Structural Analysis | Biophysics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| opengl | FASTER | Documentation, Uses, and more | ||||
| openimageio | ACES | OpenImageIO is a library for reading and writing images, and a bunch of related functionality, like dealing with image formats and color management. | Image Processing, Color Management, Library, Image Formats, Cross-Platform | Computer & Information Sciences | Computational Software | Documentation, Uses, and more |
| openjdk | Anvil Delta Expanse KyRIC |
OpenJDK (Open Java Development Kit) is a free and open-source implementation of the Java Platform, Standard Edition (Java SE). It is developed under the OpenJDK project as a collaboration between several companies and the open-source community. | Open-Source, Java Development, Software Development, Programming | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| openjpeg | ACES FASTER |
OpenJPEG is an open-source JPEG 2000 codec written in C language. It aims to provide an open-source toolkit for JPEG 2000 encoding and decoding. OpenJPEG is free software licensed under the BSD-2-Clause. | Jpeg 2000 Codec, Image Processing Software, Open-Source Software | Computer & Information Sciences | Codec | Documentation, Uses, and more |
| openldap | Expanse Ookami |
OpenLDAP is an open-source implementation of the Lightweight Directory Access Protocol (LDAP) that provides a platform-independent, stable, and high-performance LDAP server suite. It is designed to provide robust, scalable, and secure directory services for managing user authentication, access control, and directory information. | Ldap, Directory Services, Authentication, Access Control, Open Source | Computer & Information Sciences | System Software | Documentation, Uses, and more |
| openmc | FASTER | Documentation, Uses, and more | ||||
| openmm | ACES FASTER |
OpenMM is a widely-used open-source toolkit for molecular dynamics simulation. It provides a high-performance, flexible, and easy-to-use platform for the development of computationally intensive simulations of biomolecular systems. | Molecular Dynamics, Biomolecular Simulations, Computational Chemistry, Biophysics, Gpu Acceleration | Bioinformatics, Biological Sciences | Molecular Dynamics Software | Documentation, Uses, and more |
| openmpi | ACES Anvil Bridges-2 Delta FASTER KyRIC Ookami |
OpenMPI is an open-source Message Passing Interface (MPI) library that allows parallel computing on a distributed memory system. It enables high performance computing (HPC) by facilitating communication and coordination between processes running on multiple nodes. | Mpi Library, Parallel Computing, High Performance Computing, Distributed Memory System | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| openmpi/gcc/64 | Expanse | Documentation, Uses, and more | ||||
| openmpi4 | KyRIC | The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available. Description Source: https://www.open-mpi.org/ |
Library | Documentation, Uses, and more | ||
| openmx | FASTER | OpenMX is a software package for nano-scale material simulations based on density functional theories, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions. | Computational Chemistry, Materials Science | Physical Chemistry, Chemical Sciences | Quantum Chemistry Software | Documentation, Uses, and more |
| openpgm | ACES FASTER |
OpenPGM is an open-source implementation of the Pragmatic General Multicast (PGM) protocol for reliable and scalable multicast communication. It offers high performance and reliability for applications requiring multicast messaging. | Multicast Communication, Network Protocols, Open Source Software | Computer & Information Sciences | Networking | Documentation, Uses, and more |
| openpmix | Ookami | OpenPMIX is an open-source package specifically designed for multi-party computation (MPC) applications, providing efficient and secure protocols for combining data from multiple parties without revealing individual inputs. It supports a range of MPC protocols and functionalities for privacy-preserving computations. | Mpc, Privacy-Preserving Computations, Data Security, Open-Source | Computer & Information Sciences | Library/Toolkit | Documentation, Uses, and more |
| openpyxl | ACES FASTER |
Documentation, Uses, and more | ||||
| openscenegraph | ACES | OpenSceneGraph (OSG) is an open-source high-performance 3D graphics toolkit that is widely used in the fields of virtual reality, simulation, visualization, and gaming. It provides a powerful scene graph API for rapid development of interactive 3D graphics applications. | 3D Graphics, Virtual Reality, Simulation, Visualization, Gaming | Engineering & Technology | Library | Documentation, Uses, and more |
| opensees | Stampede3 | OpenSees is an open-source software framework developed for simulating the seismic response of structural and geotechnical systems. It is widely used in civil engineering for earthquake engineering research, structural analysis, and performance-based design. | Simulation, Finite Element Analysis, Earthquake Engineering, Structural Analysis, Geotechnical Engineering | Civil Engineering, Engineering & Technology | Finite Element Analysis (Fea) | Documentation, Uses, and more |
| openshmemx | DeltaAI | OpenSHMEMX is a portable implementation of the OpenSHMEM API designed to provide a high-performance, flexible, and scalable parallel programming model for symmetric multiprocessing (SMP) and massively parallel processing systems. It extends the original OpenSHMEM and aims to simplify the development of parallel applications. | Parallel Programming, High-Performance Computing, Distributed Memory Programming | Computer Science, Computer & Information Sciences | Parallel Programming Library | Documentation, Uses, and more |
| openslide | Bridges-2 | Documentation, Uses, and more | ||||
| openssh | KyRIC | OpenSSH is a suite of secure networking utilities based on the SSH protocol, providing encrypted communication sessions over a computer network using the SSH protocol. It offers secure remote login, secure file transfer, and public key authentication functionalities. | Ssh, Secure Networking, Utilities | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| openssl | ACES Anvil DeltaAI FASTER KyRIC Ookami |
OpenSSL is a robust, commercial-grade, and full-featured toolkit for the Transport Layer Security (TLS) and Secure Sockets Layer (SSL) protocols. It is also a general-purpose cryptography library. | Cryptography, Security, Encryption, Networking | Computer & Information Sciences, Other Computer & Information Sciences | Documentation, Uses, and more | |
| opensubdiv | ACES | OpenSubdiv is an open-source library that provides high-performance subdivision surface evaluation on massively parallel hardware. It generates high-quality surfaces, enabling detailed and complex geometry to be efficiently rendered and animated. | Subdivision Surface, Rendering, Animation | Computer & Information Sciences | Graphics | Documentation, Uses, and more |
| opensycl | Ookami | openSYCL is an open-source implementation of the SYCL standard, which is a higher-level programming model for developing C++ applications on heterogeneous systems with various accelerators such as GPUs, FPGAs, and other specialized processing units. It enables developers to write single-source C++ code that can target a variety of hardware accelerators without the need for low-level programming. | Programming Model, Heterogeneous Systems, Accelerators | Computer Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| operating system provided modules | KyRIC | Documentation, Uses, and more | ||||
| optax | FASTER | Documentation, Uses, and more | ||||
| optix | ACES FASTER |
OptiX is a GPU-accelerated ray tracing engine from NVIDIA that provides a programmable ray tracing pipeline for developers to build high-performance ray tracing applications. | Ray Tracing, Gpu-Accelerated, Real-Time Rendering | Computer Science, Computer & Information Sciences | Gpu Software | Documentation, Uses, and more |
| optuna | ACES FASTER |
Optuna is an open-source hyperparameter optimization framework to automate hyperparameter search with a variety of flexible and powerful features for machine learning model training. | Machine Learning, Hyperparameter Optimization, Automated Machine Learning, Optimization Framework | Computer & Information Sciences | Library | Documentation, Uses, and more |
| orca | ACES Bridges-2 Delta FASTER |
Orca is a flexible, efficient, and powerful quantum chemistry software written by Frank Neese and co-workers. It provides accurate and reliable computational simulations of molecular structures and properties based on quantum mechanical methods. | Quantum Chemistry, Computational Chemistry, Quantum Mechanics | Physical Chemistry, Chemical Sciences | Quantum Chemistry Software | Documentation, Uses, and more |
| orthofinder | FASTER | OrthoFinder is a fast and accurate tool for phylogenomic orthology and gene set inference. | Bioinformatics, Phylogenomics, Orthology, Gene Set Inference | Biological Sciences | Genome Analysis Software | Documentation, Uses, and more |
| osi | FASTER | OSI (Open System Interconnection) is a conceptual framework that standardizes the functions of a telecommunication or computing system into seven abstraction layers. It facilitates communication between different systems by defining a set of protocols to be used at each layer. | Networking, Communication, Protocol, Standardization | Computer Science, Computer & Information Sciences | Networking Software | Documentation, Uses, and more |
| osu | KyRIC | Documentation, Uses, and more | ||||
| osu-micro-benchmarks | ACES Delta FASTER |
OSU Micro-Benchmarks is a suite of parallel micro-benchmarks written in C with MPI and OpenMP implementations, designed for evaluating the performance of parallel computing systems and HPC networks. | Performance Evaluation, Hpc, Benchmarking | Engineering & Technology | Tool | Documentation, Uses, and more |
| otf2 | ACES | OTF2 is a trace format for event traces. It is mainly used for the scalable and efficient storage, transfer, and analysis of trace data generated by HPC applications. | Trace Format, Event Traces, Hpc Applications | Infrastructure & Instrumentation, Engineering & Technology | Library | Documentation, Uses, and more |
| ovito | Anvil | Documentation, Uses, and more | ||||
| p11-kit | ACES FASTER |
p11-kit is a library to manage PKCS#11 modules. It enables multiple applications to use the same PKCS#11 module in parallel, ensures that applications get access to the same serialized view of the module's state, and handles sharing access to the module state among applications. | Library, Pkcs#11, Module Management | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| p4est | Stampede3 | p4est (parallel framework for dynamic load balancing and adaptive mesh refinement) is a software library that provides support for dynamic load balancing and adaptive mesh refinement in parallel numerical simulations. It is particularly useful for solving partial differential equations on unstructured grids efficiently. | Computational Software, Library | Engineering & Technology | Library | Documentation, Uses, and more |
| p4vasp | FASTER | Documentation, Uses, and more | ||||
| p7zip | ACES Expanse FASTER Ookami |
p7zip is a command-line file archiver that supports the 7z compression format and various other archive formats. It is based on the open-source LZMA compression algorithm. | File Archiver, Compression Software, Command-Line Tool, Open-Source Software | Computer & Information Sciences | Documentation, Uses, and more | |
| padicotm | ACES | PadicoTM is a parallel discrete element method software package tailored for large-scale simulations of granular and multiphase flows. It is designed to efficiently model the behavior of particulate materials in various engineering and scientific applications. | Dem, Granular Flows, Multiphase Flows, Simulation Software | Engineering & Technology | Computational Software | Documentation, Uses, and more |
| pairtools | FASTER | Documentation, Uses, and more | ||||
| pal2nal | FASTER | Documentation, Uses, and more | ||||
| pals | Delta | Documentation, Uses, and more | ||||
| paml | FASTER | PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analysis of DNA or protein sequences using maximum likelihood. It provides a wide range of tools for evolutionary analysis and inference in a phylogenetic context. | Phylogenetics, Evolutionary Analysis, Maximum Likelihood, Phylogenetic Inference | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| pandas | FASTER | pandas is an open-source data manipulation and analysis library for Python. It provides data structures and functions that are designed to make data analysis fast and easy in Python. pandas is well-suited for working with structured data, such as tabular data, time series, and observational data. | Python Library, Data Manipulation, Data Analysis, Structured Data, Tabular Data | Informatics, Analytics & Information Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pandoc | ACES FASTER |
Documentation, Uses, and more | ||||
| pango | ACES Delta DeltaAI FASTER |
Pango is a library for layout and rendering of text, with an emphasis on internationalization. It forms the core of text and font handling for the GTK+ toolkit and is used by a variety of other open-source projects, including GNOME desktop environment. | Text Layout, Font Handling, Internationalization | Computer & Information Sciences | Text Processing | Documentation, Uses, and more |
| papi | ACES Anvil Delta DeltaAI FASTER KyRIC Ookami Stampede3 |
PAPI (Performance Application Programming Interface) is a portable and efficient API that provides a consistent interface and methodology for collecting performance counter data from the underlying hardware. | Performance Monitoring, Api, Hardware Counter | Engineering & Technology | Library | Documentation, Uses, and more |
| parabricks | ACES FASTER |
Parabricks is a GPU-accelerated toolkit that assists in fast and accurate genomic analysis. It is designed to efficiently process raw sequencing data, such as those generated by DNA sequencing technologies, for tasks like variant calling, mapping, and genome assembly. | Genomic Analysis, DNA Sequencing, Variant Calling, Gpu Acceleration | Genomics, Biological Sciences | Toolkit | Documentation, Uses, and more |
| parafly | Anvil | Parafly is a Python library for parallelizing and distributing task execution across multiple cores or nodes, aimed at improving computational efficiency for high-performance computing applications. | Parallelization, Distributed Computing, Python Library | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| parafold | ACES FASTER |
Parafold is a software tool for RNA secondary structure prediction using deep learning models. It utilizes neural networks to predict RNA secondary structures from primary sequences. | RNA Secondary Structure Prediction, Deep Learning, Neural Networks | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| parallel | ACES Anvil Delta DeltaAI Expanse FASTER |
GNU Parallel is a command-line tool for Unix-like operating systems that allows the user to execute shell scripts or commands in parallel. It is designed to simplify parallel job execution on single or multiple processors without the need for complex scripting. | Parallel Computing, Command-Line Tool, Task Scheduling | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| parallel-hashmap | FASTER | Documentation, Uses, and more | ||||
| parallel-netcdf | Anvil Bridges-2 Delta DeltaAI Stampede3 |
Parallel-NetCDF is a library providing high-performance I/O in parallel environments for big data applications with large scientific datasets. It offers parallel I/O capabilities for NetCDF files, which are commonly used in climate modeling, weather forecasting, and other scientific disciplines. | High-Performance I/O, Big Data, Parallel Computing | Earth & Environmental Sciences, Physical Sciences | I/O Library | Documentation, Uses, and more |
| parallelfold | FASTER | ParallelFold is a software tool designed for predicting RNA secondary structures in a parallel and high-performance computing environment. It implements efficient algorithms for parallelization to accelerate the prediction process. | Computational Biology, Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Prediction Tool | Documentation, Uses, and more |
| parameterized | ACES FASTER |
Documentation, Uses, and more | ||||
| parasail | FASTER | Parasail is a SIMD C library for global, semi-global, and local pairwise sequence alignments. It is optimized for typical x86 and x86-64 architectures, automatically detecting and using AVX, AVX2, and/or SSE4.1 vectorization as well as the KNC instruction set when available. Parasail includes the Smith-Waterman-Gotoh algorithm for local alignments and the Needleman-Wunsch algorithm for global alignments. | Bioinformatics, Computational Software, Hpc Tools | Biological Sciences | Library | Documentation, Uses, and more |
| paraview | ACES Anvil Delta FASTER Stampede3 |
ParaView is an open-source, multi-platform data analysis and visualization application. It is designed to handle large data sets and offers a wide range of visualization techniques to analyze and interact with the data. | Visualization, Data Analysis, Open-Source, Multi-Platform | Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences | Data Visualization | Documentation, Uses, and more |
| paraview-osmesa | Stampede3 | Documentation, Uses, and more | ||||
| parmed | FASTER | Documentation, Uses, and more | ||||
| parmetis | ACES Delta FASTER Stampede3 |
ParMETIS is an MPI-based parallel graph partitioning and sparse matrix ordering library designed for efficiently solving large, sparse graph problems. It provides high-performance graph partitioning, matrix reordering, and fill-reducing matrix ordering capabilities for a wide range of scientific computing applications. | Graph Partitioning, Sparse Matrix Ordering, Scientific Computing, Parallel Computing | Computer Science, Computer & Information Sciences | Computational Tool | Documentation, Uses, and more |
| parpack | Stampede3 | PARPACK is a software library for solving large scale eigenvalue problems. It is specifically designed to compute a few eigenvalues and corresponding eigenvectors of large sparse matrices. | Eigenvalue Problems, Sparse Matrices, Numerical Linear Algebra | Mathematics | Library | Documentation, Uses, and more |
| parsl | ACES | Documentation, Uses, and more | ||||
| parsnp | FASTER | parsnp is a software tool used for rapid core-genome alignment and SNP detection in whole-genome sequencing data. It is particularly designed for comparative genomics studies to identify genetic variations and evolutionary relationships among bacterial genomes. | Genomics, Bioinformatics, Sequencing, Evolutionary Biology | Biological Sciences | Genomics Analysis Tool | Documentation, Uses, and more |
| pasa | ACES FASTER |
Documentation, Uses, and more | ||||
| patchelf | ACES FASTER Ookami |
PatchELF is a simple utility for modifying the dynamic linker and run-time library paths in executable files. | Dependency Management, Executable Modification, Dynamic Linker Paths | Computer & Information Sciences | Library Management | Documentation, Uses, and more |
| paup | FASTER | Documentation, Uses, and more | ||||
| pax-utils | Ookami | pax-utils is a set of utilities that enable examination and manipulation of ELF (Executable and Linkable Format) files created for Linux systems. These tools are primarily used for analyzing and modifying various attributes of ELF binaries. | Elf Files, Binary Analysis, Security Tools, Linux | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| pblat | ACES | pblat (Parallel BLAT) is a software tool that efficiently aligns biological sequences to a reference genome by using the BLAT algorithm in a parallel computing framework. It is specifically designed for high-throughput sequence analysis tasks, offering improved speed and scalability for large-scale genomic analyses. | Bioinformatics, Sequence Alignment, Genomics, Parallel Computing | Genomics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| pcangsd | FASTER | PCAngsd is a Python-based software tool used for the estimation of demographic history from whole-genome sequencing data. It is designed to infer the demographic history of populations, particularly focusing on the estimation of historical population size changes and divergence times. | Population Genetics, Genomic Data Analysis | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| pciutils | Expanse | pciutils is a set of utilities for displaying information about PCI buses in the system and devices connected to them. It provides various tools for configuration, diagnostics, and monitoring of PCI devices in Linux systems. | Pci Management, System Utilities, Linux Tools | Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| pcre | ACES Anvil DeltaAI FASTER |
Perl Compatible Regular Expressions (PCRE) is a library for pattern matching with regular expressions. It implements the functionality of the regular expression library in Perl and provides support for Perl-style regular expressions in many programming languages. | Regular Expressions, Pattern Matching, Library | Biology, Computer & Information Sciences | Runtime Library | Documentation, Uses, and more |
| pcre2 | ACES DeltaAI FASTER KyRIC Stampede3 |
PCRE2 is a C library implementing Perl-compatible regular expressions. It is a reimplementation of PCRE but with a different API that is designed to be compatible with Perl 5. It provides a regular expression matching engine that supports Perl-style patterns while also providing some features not found in Perl, such as matching up to 2^16 code units. | Regular Expressions, Text Processing, Pattern Matching | Biology, Computer & Information Sciences | C Library | Documentation, Uses, and more |
| pdal | ACES FASTER |
PDAL is an open-source library for point cloud processing and data management. It offers a variety of tools and pipelines for manipulating geospatial data in the form of point clouds. | Point Cloud, Geospatial Data, Lidar, Gis, Data Processing | Other Natural Sciences | Point Cloud Processing | Documentation, Uses, and more |
| pdm | FASTER | Documentation, Uses, and more | ||||
| pdt | ACES | Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers, analysts, and creating tools for source code understanding. | Software, Programming, Source Code, Analysis | Computer & Information Sciences | Tools | Documentation, Uses, and more |
| pdtoolkit | KyRIC | pdtoolkit is a Python library for exploratory data analysis and preprocessing of tabular data. It provides various tools and functions for data cleaning, transformation, feature selection, and visualization. | Python Library, Exploratory Data Analysis, Data Preprocessing, Feature Selection, Visualization | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pepper | FASTER | Documentation, Uses, and more | ||||
| perftools | DeltaAI | Perftools is a collection of performance analysis tools designed to help developers optimize their software by identifying performance bottlenecks and areas for improvement. It includes a suite of profiling tools that can be used to analyze CPU and memory usage, as well as identify hotspots in code. | Performance Analysis, Optimization, Profiling | Engineering & Technology | Performance Analysis Tools | Documentation, Uses, and more |
| perftools-base | Delta DeltaAI |
perftools is a collection of performance analysis tools for Linux-based systems. perftools-base is the base package of perftools which includes basic performance analysis tools for profiling CPU and memory usage. | Performance Analysis, Profiling, Linux | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| perftools-lite | DeltaAI | Perftools lite is a set of performance analysis tools designed for lightweight profiling and tracing of applications. It provides insights into the performance of software applications to help optimize and improve efficiency. | Performance Analysis, Profiling, Tracing | Computer Science, Computer & Information Sciences | Software Tool | Documentation, Uses, and more |
| perftools-lite-events | DeltaAI | Perftools Lite (PTL) provides a framework for lightweight performance analysis of parallel applications. It allows users to collect and analyze performance data to identify bottlenecks and optimize code performance. PTL focuses on event-based performance analysis to monitor and measure the execution behavior of parallel applications. | Performance Analysis, Parallel Applications, Optimization | Computer & Information Sciences | Compiler/Profiler | Documentation, Uses, and more |
| perftools-lite-gpu | DeltaAI | Perftools-lite-gpu is a lightweight performance analysis tool designed for GPU applications. It allows developers to analyze the performance of their GPU-accelerated applications by providing insightful metrics and visualizations. | Performance Analysis, Gpu Applications, Metrics, Visualization | Engineering & Technology | Performance Analysis Tool | Documentation, Uses, and more |
| perftools-lite-hbm | DeltaAI | PerfTools-Lite-HBM is a performance analysis tool specifically designed for profiling applications running on High Bandwidth Memory (HBM) systems. It provides insights into memory access patterns, cache behavior, and overall performance characteristics of HBM-enabled applications. | Performance Analysis, Memory Profiling, Hbm Systems, High Bandwidth Memory, Optimization | Engineering & Technology | Profiler | Documentation, Uses, and more |
| perftools-lite-loops | DeltaAI | The perftools-lite-loops software is a performance monitoring tool that focuses on analyzing loop-level performance in applications. It is designed to provide detailed insights into loop optimizations, dependencies, and potential performance bottlenecks in code. | Performance Monitoring, Optimization, Debugging | Computer & Information Sciences | Analysis Tool | Documentation, Uses, and more |
| perftools-preload | DeltaAI | perftools-preload is a tool designed to optimize and profile code performance by collecting runtime statistics, such as CPU utilization, memory usage, and function call traces. It is particularly useful for identifying performance bottlenecks and optimizing code for improved efficiency. | Performance Optimization, Code Profiling, Software Performance, Debugging | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| perl | ACES Anvil DeltaAI FASTER KyRIC |
Perl is a high-level, general-purpose, interpreted, dynamic programming language known for its powerful text-processing features and used for a wide range of tasks including web development, system administration, and network programming. | Programming Language, Text Processing, Scripting, Web Development, System Administration | Computer & Information Sciences | Programming Language | Documentation, Uses, and more |
| perl-bioperl | Anvil | BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. | Documentation, Uses, and more | |||
| perl-bundle-cpan | ACES FASTER |
A set of common packages from CPAN | Documentation, Uses, and more | |||
| perl-bundle1-cpan | ACES FASTER |
A collection of Perl modules and libraries available on CPAN (Comprehensive Perl Archive Network) bundled together for easy installation and management. | Software Bundle, Perl Modules, Code Libraries | Computer & Information Sciences | Programming Libraries | Documentation, Uses, and more |
| perl-bundle2-cpan | ACES | perl-bundle2-cpan is a Perl module that allows for the installation of multiple CPAN modules in one go, making it easier to manage dependencies and streamline the process of installing Perl modules. | Perl, Cpan, Dependency Management, Module Installation | Computer Science, Computer & Information Sciences | Package | Documentation, Uses, and more |
| petsc | ACES Anvil Delta DeltaAI FASTER Ookami Stampede3 |
PETSc, the Portable, Extensible Toolkit for Scientific Computation, is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | Scientific Computing, Computational Science, Numerical Analysis | Natural Sciences | Library | Documentation, Uses, and more |
| petsc4py | ACES | Documentation, Uses, and more | ||||
| pfft | ACES FASTER |
Documentation, Uses, and more | ||||
| pftoolsv3 | FASTER | pftoolsv3 is a software suite that provides a collection of tools for analyzing and visualizing data related to particle filtering methods. It is designed to assist researchers and practitioners in the field of statistical signal processing and Bayesian inference. | Particle Filtering, Statistical Signal Processing, Bayesian Inference, Data Analysis, Visualization | Statistics & Probability, Mathematics | Research Tool | Documentation, Uses, and more |
| pgdspider | FASTER | Documentation, Uses, and more | ||||
| pgenomics | FASTER | Documentation, Uses, and more | ||||
| pharokka | FASTER | Documentation, Uses, and more | ||||
| phast | FASTER | PHAST (PHylogenetic Analysis with Space/Time models) is a software package for comparative and evolutionary genomics. It is designed for analyzing patterns of evolutionary conservation and acceleration in multiple alignments of genomic sequences. | Genomics, Phylogenetics, Evolutionary Biology, Bioinformatics | Genomics, Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| phdf5 | Bridges-2 Stampede3 |
ph5util provides utilities for reading, writing, and manipulating PHDF5 files. PHDF5 is a parallel I/O file format based on the HDF5 file format and is used for storing large datasets efficiently across distributed storage systems. | Parallel I/O, Phdf5, Hdf5, Large Datasets | Computer & Information Sciences | File Format | Documentation, Uses, and more |
| phipack | FASTER | Phipack is a software package for the analysis of site-specific amino acid substitutions within multiple sequence alignments. It uses statistical methods to estimate selection pressure at individual sites, identify positive selection on specific branches of a phylogenetic tree, and detect recombination events. | Bioinformatics, Computational Biology | Genetics, Biological Sciences | Analytics Tool | Documentation, Uses, and more |
| phobius | FASTER | Documentation, Uses, and more | ||||
| php | FASTER | PHP is a popular general-purpose scripting language that is especially suited to web development. It is a server-side scripting language embedded in HTML. | Programming Language, Web Development | Computer & Information Sciences | Scripting Language | Documentation, Uses, and more |
| phylip | ACES FASTER |
Documentation, Uses, and more | ||||
| phylip-suite | Bridges-2 | PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables. Description Source: https://phylipweb.github.io/phylip/ |
Documentation, Uses, and more | |||
| phyloflash | FASTER | Documentation, Uses, and more | ||||
| phylophlan | FASTER | Documentation, Uses, and more | ||||
| phyml | FASTER | Documentation, Uses, and more | ||||
| physics-tenpy | ACES FASTER |
TeNPy (short for ‘Tensor Network Python’) is a Python library for the simulation of strongly correlated quantum systems with tensor networks. Description Source: https://pypi.org/project/physics-tenpy/ |
Documentation, Uses, and more | |||
| picard | ACES Anvil Bridges-2 Delta FASTER |
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. It is primarily used for processing and analyzing next-generation sequencing (NGS) data in genomics. | Bioinformatics, Ngs, Hts, Sequencing Data, Sam, Bam, Vcf | Genomics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| pigz | ACES Expanse FASTER |
pigz, which stands for parallel implementation of gzip, is a compression utility that uses multiple processors and cores to compress files quickly and efficiently. It is compatible with gzip and gunzip, allowing for seamless integration with existing gzip workflows. | Compression, Parallel Processing, Utility, Command-Line Tool | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| pillow | ACES FASTER |
Pillow is a powerful Python Imaging Library (PIL) replacement that adds image processing capabilities to your Python interpreter. | Image Processing, Python Library | Computer & Information Sciences, Software Engineering, Systems & Development | Library | Documentation, Uses, and more |
| pillow-simd | ACES FASTER |
pillow-simd is an optimized fork of Python imaging library (PIL) with SIMD support, designed to enhance image processing capabilities with improved performance. | Image Processing, Python Library, Optimization | Computer & Information Sciences | Image Processing | Documentation, Uses, and more |
| pilon | Bridges-2 FASTER |
Pilon is a software package that automates the improvement of draft assemblies of microbial genomes, using information from multiple sources to correct draft assemblies. | Genome Assembly, Genomics, Bioinformatics, Computational Biology | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| pint | FASTER | Documentation, Uses, and more | ||||
| pioman | ACES | Pioman is a Python package that provides tools for parallel input and output (IO) management. It aims to optimize IO performance in high-performance computing (HPC) environments by enabling efficient reading and writing of large datasets. Pioman is particularly useful for scientific simulations and data analysis workflows that involve heavy IO operations. | Python Library, Hpc Tool, Io Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pipenv | ACES FASTER |
Documentation, Uses, and more | ||||
| pixman | ACES Anvil DeltaAI FASTER |
Pixman is a low-level software library for pixel manipulation, providing software acceleration for numerous rendering operations. It is used primarily by projects requiring high-quality rendering such as the X server, Cairo, the GTK+ toolkit, and more. | Pixel Manipulation, Rendering, Software Library, Performance | Computer & Information Sciences | Graphics Library | Documentation, Uses, and more |
| pkg-config | ACES FASTER |
pkg-config is a helper tool used when compiling applications and libraries. It helps to manage compiler and linker flags for libraries in the system. It simplifies the process of compiling and linking against libraries. | Compilation, Library Management, Build Process | Engineering & Technology | Utility | Documentation, Uses, and more |
| pkgconf | ACES DeltaAI FASTER KyRIC |
pkgconf is a package configuration system. It helps to provide a uniform and system-agnostic API for the management of build and link flags. It replaces the functionality of pkg-config. | Package Configuration, Build Flags, Link Flags, System-Agnostic | Computer & Information Sciences | Package Configuration | Documentation, Uses, and more |
| pkgconfig | ACES FASTER |
pkg-config is a helper tool used when compiling applications and libraries. It helps in specifying compilation options by providing the compiler options needed to use a library. It also provides information about installed libraries. | Compilation, Library Management, Software Development | Engineering & Technology | Tool | Documentation, Uses, and more |
| platanus | FASTER | Documentation, Uses, and more | ||||
| platypus | FASTER | Platypus is a highly flexible variant detection and visualization software for short-read sequencing. It is particularly designed for calling single nucleotide variants (SNVs), small insertions and deletions (indels), and larger deletions from mapped short-read data. | Variant Detection, Sequencing, Bioinformatics | Genetics, Biological Sciences | Variant Detection Tool | Documentation, Uses, and more |
| plink | ACES FASTER |
PLINK (whole-genome association analysis toolset) is an open-source whole genome association analysis toolset designed to perform a range of basic, large-scale analyses in a computationally efficient manner. It enables users to carry out a variety of tasks, such as quality control, data management, and statistical analysis of genotypic data. | Genetic Analysis, Genomic Data Analysis, Gwas, Genetic Epidemiology | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| plink2 | Delta | PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). | Genomics, Association Analysis, Genotype-Phenotype Data | Biological Sciences | Tool | Documentation, Uses, and more |
| plotly.py | ACES FASTER |
Plotly.py is an open-source Python graphing library that makes interactive, publication-quality graphs online. It allows users to create interactive plots and dashboards using Python, with a high degree of customization and interactivity. | Data Visualization, Graphing Library, Python Library | Computer & Information Sciences | Graphing Library | Documentation, Uses, and more |
| plumed | ACES Bridges-2 Delta FASTER Ookami |
PLUMED is an open-source library for free energy calculations in molecular dynamics simulations. It allows for the easy and flexible implementation of enhanced sampling techniques and the calculation of various collective variables. | Molecular Dynamics, Enhanced Sampling, Free Energy Calculations, Collective Variables | Chemistry, Biological Sciences | Library | Documentation, Uses, and more |
| ply | FASTER | Ply is a pure-Python implementation of the popular Lex and Yacc parsing tools. It is designed to simplify the process of writing lexers and parsers in Python, providing a high-level, object-oriented interface that makes it easy to define grammars directly in the code. | Parser, Lexer, Python, Parsing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pmi | Delta DeltaAI |
PMI (Project Management Institute) is a global nonprofit professional organization for project management. It offers various certifications, standards, and resources for project managers. | Documentation, Uses, and more | |||
| pmix | ACES FASTER KyRIC Ookami |
The Process Management Interface (PMIx) is an abstract interface for managing the data and resources associated with managing parallel processes. It provides a framework and services for coordinating data exchange and interaction amongst parallel processes in high-performance computing environments. | Process Management, Parallel Computing, High-Performance Computing, Data Exchange, Resource Management, Scalability | Engineering & Technology | Hpc Tool | Documentation, Uses, and more |
| pnetcdf | ACES FASTER Stampede3 |
PnetCDF is a parallel I/O library for accessing NetCDF files in parallel. It is specifically designed to address the scalability and performance limitations of serial NetCDF I/O by providing parallel I/O support. | Parallel I/O, Netcdf Files, Scalability, Performance | Physical Sciences | I/O Library | Documentation, Uses, and more |
| pocl | ACES FASTER |
Portable Computing Language (pocl) is an open-source implementation of the OpenCL standard which aims to provide a portable programming layer for execution on various devices including CPUs, GPUs, and FPGAs. It enables developers to write parallel programs that can be executed efficiently across different hardware platforms. | Opencl, Parallel Computing, Hardware Acceleration | Computer Science, Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| pod5-file-format | FASTER | Documentation, Uses, and more | ||||
| poetry | ACES FASTER |
Poetry is a dependency management and packaging tool for Python projects. It allows you to declare and manage project dependencies, create virtual environments, build and publish packages, and more. | Dependency Management, Packaging, Python | Computer & Information Sciences | Package Manager | Documentation, Uses, and more |
| polars | ACES FASTER |
Documentation, Uses, and more | ||||
| poppler | ACES FASTER |
Poppler is a software utility library that is used to render PDF documents. It is a PDF rendering library based on the xpdf-3.0 code base. It provides various command-line utilities for working with PDF files as well. | Pdf Rendering, Pdf Manipulation, Pdf Parsing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| popt | FASTER KyRIC |
popt is a C library for parsing command line options. | Command Line Options, C Library | Computer & Information Sciences | Command Line Option Parser | Documentation, Uses, and more |
| porechop | Bridges-2 FASTER |
Documentation, Uses, and more | ||||
| portmidi | ACES | Documentation, Uses, and more | ||||
| posix2ime | Delta | posix2ime is a software tool that converts POSIX timestamp to IME-mode timestamp in Linux systems. It is particularly useful for converting timestamps in the Input Method Editor (IME) mode, commonly used for inputting non-Latin characters in Asian languages. | Timestamp Conversion, Linux Software, Ime-Mode Timestamp | Computer & Information Sciences | Conversion Tool | Documentation, Uses, and more |
| postgresql | ACES FASTER |
PostgreSQL is a powerful, open-source relational database management system known for its reliability, robustness, and performance. It offers advanced features such as multi-version concurrency control, point-in-time recovery, and full ACID compliance. | Database Management, Relational Database, Open Source, Data Management | Documentation, Uses, and more | ||
| pov-ray | ACES FASTER |
POV-Ray (Persistence of Vision Raytracer) is a high-quality three-dimensional graphics tool that creates stunning photorealistic images using ray tracing techniques. It is a free, open-source software package that allows users to design detailed scenes using a specialized scripting language. | 3D Graphics, Ray Tracing, Open-Source, Visualization | Computer Science | Visualization Software | Documentation, Uses, and more |
| pplacer | ACES FASTER |
pplacer is a phylogenetic placement tool that places query sequences on a fixed reference phylogenetic tree while simultaneously estimating their likelihoods. It is particularly useful for analyzing large collections of short reads, such as those generated from next-generation sequencing technologies. | Phylogenetic Analysis, Sequence Placement, Phylogenetic Tree, Likelihood Estimation | Biological Sciences | Tool | Documentation, Uses, and more |
| prank | ACES FASTER |
PRANK is a probabilistic multiple sequence alignment program for DNA, codon and amino-acid sequences. It constructs multiple alignments by aligning sequences pairwise based on local alignment and phylogenetic information. | Sequence Alignment, Bioinformatics, Genomics, Phylogenetics | Genetics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| precice | Stampede3 | Documentation, Uses, and more | ||||
| preseq | FASTER | Documentation, Uses, and more | ||||
| prgenv | Delta DeltaAI |
Documentation, Uses, and more | ||||
| prgenv-gnu | Delta DeltaAI |
The prgenv-gnu is a programming environment module that provides the GNU compiler collection (GCC) for compiling and running codes. It sets up the environment variables needed to compile and run programs using the GNU compilers. | Programming Environment, Gnu Compiler Collection (Gcc) | Computer & Information Sciences, Software Engineering, Systems & Development | Compiler | Documentation, Uses, and more |
| prgenv-nvhpc | Delta DeltaAI |
The prgenv-nvhpc module is part of the NVIDIA HPC SDK that provides an environment for compiling and running HPC applications on NVIDIA GPUs. It includes compilers, libraries, tools, and runtime support optimized for high-performance computing workloads. | Hpc, Compiler, Gpu Computing, High-Performance Computing | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| prgenv-nvidia | Delta DeltaAI |
prgenv-nvidia is a software environment that provides compilers and tools optimized for NVIDIA GPUs, allowing users to develop and execute GPU-accelerated applications efficiently. | Software Environment, Compilers, Gpu Computing, Nvidia | Computational Science, Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| printproto | DeltaAI | Documentation, Uses, and more | ||||
| probtorch | FASTER | Probabilistic Torch is a deep probabilistic programming library built on PyTorch that combines the strengths of deep learning and probabilistic graphical models. It enables users to easily specify and train differentiable generative models for uncertainty estimation. | Probabilistic Programming, Deep Learning, Pytorch | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Open Source | Documentation, Uses, and more |
| prodigal | ACES Bridges-2 FASTER |
Prodigal is a microbial gene finding program that identifies protein-coding regions in microbial genomes. It uses a combination of intrinsic and extrinsic signals to accurately predict genes in bacterial and archaeal genomes. | Gene Prediction, Microbial Genomes | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| prody | FASTER | Documentation, Uses, and more | ||||
| proj | ACES Anvil Delta DeltaAI FASTER Ookami Stampede3 |
PROJ is a standard Unix filter function designed to convert geographic longitude and latitude coordinates into Cartesian coordinates. It is widely used in geospatial applications for coordinate transformation and map projection. | Geospatial, Coordinate Transformation, Map Projection | Geography, Earth Sciences | Coordinate Transformation Tool | Documentation, Uses, and more |
| prokka | ACES Bridges-2 FASTER |
Prokka is a software tool for rapid prokaryotic genome annotation. It annotates bacterial, archaeal, and viral genomes quickly and easily. Prokka performs a comprehensive annotation that includes gene prediction, functional annotation, and other genomic features. | Genome Annotation, Bioinformatics, Genomics | Genetics, Biological Sciences | Annotation Tool | Documentation, Uses, and more |
| protobuf | ACES Anvil FASTER |
Protocol buffers are a language- and platform-neutral extensible mechanism for serializing structured data. It enables you to define data structures in a JSON-like format and automatically generate code to serialize and deserialize them in a variety of languages. | Serialization, Data Interchange, Code Generation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| protobuf-python | ACES FASTER |
protobuf-python is a Python library for Protocol Buffers, Google's language-neutral, platform-neutral extensible mechanism for serializing structured data. | Data Serialization, Binary Encoding, Data Validation, Structured Data, Extensible | Computer & Information Sciences | Serialization | Documentation, Uses, and more |
| protoc | FASTER | Documentation, Uses, and more | ||||
| prrte | ACES FASTER |
PRRTE (Proactive Resilience and Real-Time Executor) is a fault tolerance framework designed to provide fault tolerance capabilities to complex, high-performance computing (HPC) applications. It focuses on enabling applications to run to completion in the presence of faults by providing various resilience strategies. | Fault Tolerance, Hpc, Resilience, Real-Time Execution | Engineering & Technology | Framework | Documentation, Uses, and more |
| prun job launch utility | KyRIC | Documentation, Uses, and more | ||||
| pscom | FASTER | pscom is a Python library for process-based communication. It provides tools for easy communication between different processes, making it simple to pass messages and data between them. | Python Library, Process Communication, Inter-Process Communication | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| psutil | FASTER | Documentation, Uses, and more | ||||
| psycopg | FASTER | Documentation, Uses, and more | ||||
| psycopg2 | ACES FASTER |
Psycopg is a popular PostgreSQL database adapter for the Python programming language. It provides a robust, efficient, and well-supported interface for interacting with PostgreSQL databases from Python applications. | Python Library, Database Adapter, Postgresql, Data Management | Computer & Information Sciences | Database Adapter | Documentation, Uses, and more |
| ptex | ACES | A high-quality Japanese typesetting system based on TeX that is specifically optimized for the Japanese language. | Typesetting, Tex, Japanese Language | Languages & Literature, Humanities | Typesetting Software | Documentation, Uses, and more |
| pugixml | ACES FASTER |
pugixml is a lightweight C++ XML processing library that consists of a simple and intuitive API. It is designed to be easy to integrate with other projects and provides efficient and fast XML parsing capabilities. | Xml Processing, C++ Library, Xpath, Parsing | Computer & Information Sciences | Xml Processing | Documentation, Uses, and more |
| puk | ACES | PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately. | Documentation, Uses, and more | |||
| pukabi | ACES | Pukabi is a bioinformatics tool used for analyzing and visualizing phylogenetic trees. | Bioinformatics, Phylogenetics, Tree Visualization | Biological Sciences | Documentation, Uses, and more | |
| pullseq | FASTER | pullseq is a tool for extracting sequence data from a multi-FASTA file based on sequence identifiers. It can extract sequences by exact match, partial match, regular expression, and invert match. It is particularly useful for subsetting sequences from large sequence datasets. | Bioinformatics, Sequence Analysis | Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| pulp | FASTER | Documentation, Uses, and more | ||||
| pulseaudio | FASTER | Documentation, Uses, and more | ||||
| pv | FASTER | PV (PVS-Studio) is a static code analysis tool that performs comprehensive code inspection to detect bugs and potential vulnerabilities in C, C++, C#, and Java code. | Static Code Analysis, Software Security, Programming | Documentation, Uses, and more | ||
| pwanalyzer | Ookami | PWAnalyzer is a software tool for analyzing protein-ligand interactions through molecular docking simulations. It allows users to study the binding modes and affinity of small molecules to target proteins, aiding in drug discovery and design. | Protein-Ligand Interactions, Molecular Docking, Drug Discovery, Bioinformatics | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| py-cpuinfo | ACES FASTER |
py-cpuinfo is a Python library to get CPU information by parsing data from /proc/cpuinfo. It provides information about the CPU and its features. | Python Library, System Information, Cpu Information | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| py-cutadapt | Anvil | py-cutadapt is a Python package for preprocessing high-throughput sequencing data. It trims adapter sequences, removes low-quality bases, and filters out reads that do not meet specified quality thresholds. | Bioinformatics, Sequencing Data Processing, Python Package | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| py-cython | DeltaAI KyRIC |
Py-Cython is a compiler for writing C extensions for the Python language. It allows for combining Python and C code seamlessly to improve performance and efficiency. | Compiler, Python Library, Performance Optimization | Computer & Information Sciences | Development Tool | Documentation, Uses, and more |
| py-flit-core | DeltaAI | Documentation, Uses, and more | ||||
| py-gpaw | Anvil | Documentation, Uses, and more | ||||
| py-htseq | Anvil | Py-htseq is a high-throughput sequencing (HTS) analysis tool in Python designed to process and analyze mapped sequence data, particularly for RNA-seq experiments. It facilitates gene expression analysis by counting reads that align to features in the reference genome or transcriptome. | Hts Analysis, RNA-Seq, Sequence Data Processing, Gene Expression, Transcriptomics | Bioinformatics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| py-meson-python | DeltaAI | Documentation, Uses, and more | ||||
| py-mpi4py | Anvil | py-mpi4py is a Python interface to the Message Passing Interface (MPI) standard for parallel computing, allowing users to utilize MPI functionality within Python scripts and applications. | Python, Mpi, Parallel Computing | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| py-numpy | Bridges-2 DeltaAI |
Python Library | Documentation, Uses, and more | |||
| py-packaging | DeltaAI | Documentation, Uses, and more | ||||
| py-pip | DeltaAI | py-pip is the official installer for Python packages from the Python Package Index (PyPI). It is used to install and manage software packages written in Python. | Package Management, Python, Software Installation | Computer & Information Sciences, Software Engineering, Systems & Development | Package Management | Documentation, Uses, and more |
| py-pyproject-metadata | DeltaAI | Documentation, Uses, and more | ||||
| py-setuptools | DeltaAI KyRIC |
Setuptools is a package development process library designed to facilitate development and distribution of Python projects. It provides a common approach for managing project dependencies, packaging, and installation processes. | Python, Package Development, Distribution, Dependency Management | Computer Science, Computer & Information Sciences | Package Management | Documentation, Uses, and more |
| py-wheel | DeltaAI | Documentation, Uses, and more | ||||
| py3dmol | ACES FASTER |
Py3Dmol is a Python library that provides a simple way to use the 3Dmol.js molecular viewer in Jupyter notebooks or Python scripts. It enables interactive visualization of molecular structures and is particularly useful for educational purposes and research in chemistry, biochemistry, and structural biology. | Molecular Visualization, Python Library | Chemical Sciences, Biological Sciences | Python Library | Documentation, Uses, and more |
| pybedtools | FASTER | pybedtools is a Python wrapper for BEDTools, a powerful software suite for genomic arithmetic. It allows to manipulate genomic data in multiple file formats and integrate with other Python libraries for bioinformatics analysis. | Genomics, Bioinformatics, Python, Bedtools | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| pybigwig | FASTER | pyBigWig is a Python interface for working with BigWig files, a binary format for efficiently storing genome-wide signal data. | Bigwig Files, Genome-Wide Signal Data, Python Interface | Biological Sciences | Library | Documentation, Uses, and more |
| pybind11 | ACES FASTER |
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings for C++ libraries. It provides seamless interoperability between C++11 and Python without the need for boilerplate code or external tools. | Software Development, Python Library, C++ Integration, Header-Only Library | Computer & Information Sciences | Interoperability | Documentation, Uses, and more |
| pybiolib | ACES FASTER |
Documentation, Uses, and more | ||||
| pycairo | ACES FASTER |
Pycairo is a set of Python bindings for the Cairo graphics library. It allows Python applications to use the powerful vector graphics capabilities provided by Cairo for creating high-quality 2D graphics and illustrations. | Python, Graphics, 2D Graphics, Illustrations | Computer & Information Sciences | Visualization Library | Documentation, Uses, and more |
| pycharm | FASTER | PyCharm is an Integrated Development Environment (IDE) used for programming in Python. It provides a range of tools for Python development, such as code completion, code inspection, a debugger, version control system integration, and support for web development with Django and Data Science with Anaconda. | Ide, Python, Development, Programming | Computer & Information Sciences | Integrated Development Environment | Documentation, Uses, and more |
| pycodestyle | FASTER | Documentation, Uses, and more | ||||
| pycuda | ACES FASTER |
PyCUDA is a Python library that enables easy access to NVIDIA's CUDA parallel computation API directly from Python. It allows for seamless integration of GPU computation into Python code, providing a high-level interface to CUDA operations. | Python Library, Gpu Computing, Parallel Processing | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pycurl | ACES FASTER |
Documentation, Uses, and more | ||||
| pydantic | ACES FASTER |
Pydantic is a data validation and settings management library in Python that provides data validation using Python type annotations. It enforces type hints at runtime, allowing you to define JSON-like data structures with Python types. | Python Library, Data Validation, Settings Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pydicom | ACES | pydicom is a Python library for working with DICOM files and data. It provides tools for reading, modifying, and writing DICOM files, as well as accessing DICOM data elements and metadata. | Python Library, Dicom Data, Medical Imaging | Medical & Health Sciences | Library | Documentation, Uses, and more |
| pydot | FASTER | Documentation, Uses, and more | ||||
| pyem | FASTER | Documentation, Uses, and more | ||||
| pyfaidx | ACES FASTER |
pyfaidx is a Python library that enables efficient random access to genome FASTA files in both uncompressed and gzipped formats. It provides a simple interface for indexing and querying sequences from FASTA files. | Python Library, Genome Analysis, Bioinformatics | Biological Sciences | Genomics | Documentation, Uses, and more |
| pyfftw | FASTER | Documentation, Uses, and more | ||||
| pyflakes | FASTER | Documentation, Uses, and more | ||||
| pyfr | ACES | PyFR is an open-source Python-based framework for solving fluid dynamics problems on many-core architectures. | Fluid Dynamics, Finite Element Method, Computational Fluid Dynamics, High-Performance Computing | Fluid Dynamics, Physical Sciences | Framework | Documentation, Uses, and more |
| pygame | ACES | Documentation, Uses, and more | ||||
| pygenometracks | FASTER | pyGenomeTracks is a Python package for plotting high quality and highly customizable visualizations of genomic data. It allows users to create complex, publication-ready figures to explore and represent genomics data effectively. | Genomics, Data Visualization, Python, Genomic Data Analysis | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| pygobject | ACES FASTER |
PyGObject is a Python module that enables developers to access GObject-based libraries in Python. It allows Python code to interact with and use functionalities provided by libraries written in the GObject introspection format. | Python, Programming, Gobject-Based Libraries, Development | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pygraphviz | FASTER | Documentation, Uses, and more | ||||
| pylauncher | Stampede3 | Documentation, Uses, and more | ||||
| pymatgen | FASTER | Documentation, Uses, and more | ||||
| pymc3 | FASTER | PyMC3 is a Python library for probabilistic programming that uses Bayesian statistical modeling to perform probabilistic inference. | Python Library, Probabilistic Programming, Bayesian Statistics | Statistics & Probability, Mathematics | Library | Documentation, Uses, and more |
| pymol | FASTER | Documentation, Uses, and more | ||||
| pyomo | FASTER | Pyomo is an open-source software package for formulating and solving mathematical optimization problems. It is a Python-based modeling language that allows users to formulate optimization problems in a natural, algebraic syntax. | Optimization, Mathematical Modeling, Python Library | Applied Mathematics, Mathematics | Modeling & Optimization Tool | Documentation, Uses, and more |
| pyopencl | FASTER | PyOpenCL lets you access GPUs and other massively parallel compute devices by using the Open Computing Language (OpenCL). The package is built on top of the OpenCL C API and enables Python scripts to easily make full use of compute devices like GPUs, TPUs, and other accelerators. | Programming, Parallel Computing, Gpu Acceleration | Computer & Information Sciences, Other Computer & Information Sciences | Python Package | Documentation, Uses, and more |
| pyopengl | ACES FASTER |
PyOpenGL is a cross-platform open source Python binding to OpenGL and related APIs that provides access to high-performance 2D and 3D graphics rendering capabilities. It allows developers to utilize the full feature set of OpenGL within Python applications. | Graphics, Opengl, Python, 2D, 3D, Rendering | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| pyparsing | FASTER | Documentation, Uses, and more | ||||
| pyproj | ACES FASTER |
Pyproj is a Python interface to the PROJ library for cartographic projections and coordinate transformations. | Python Library, Geospatial Analysis, Cartographic Projections, Coordinate Transformations | Earth & Environmental Sciences | Geospatial Analysis Software | Documentation, Uses, and more |
| pypy | FASTER | PyPy is a fast, compliant alternative implementation of the Python programming language. It aims to provide a high-performance, flexible, and efficient interpreter for Python, while maintaining compatibility with the CPython reference implementation. | Python Interpreter, Alternative Implementation, Just-In-Time Compilation, High Performance | Computer & Information Sciences | Programming Language Implementation | Documentation, Uses, and more |
| pyqt-builder | FASTER | Documentation, Uses, and more | ||||
| pyqt5 | ACES FASTER |
PyQt5 is a comprehensive set of Python bindings for the Qt application framework developed by Riverbank Computing. It allows Python programmers to create desktop applications with rich graphical user interfaces (GUIs) using Qt tools and libraries. | Python, Gui, Qt, Desktop Applications | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pyro-api | FASTER | Pyro-API is a Python package that provides an Application Programming Interface (API) for interacting with the Pyro library. Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch. Pyro-API simplifies the process of building and training probabilistic models using Pyro by providing an intuitive and high-level API. | Python Library, Probabilistic Programming, Deep Learning | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pyro-ppl | FASTER | Pyro is a universal probabilistic programming language (PPL) built on top of PyTorch. It is designed to enable flexible and expressive deep probabilistic modeling, variational inference, and probabilistic programming. | Probabilistic Programming Language, Deep Learning, Variational Inference, Pytorch | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Machine Learning Tool | Documentation, Uses, and more |
| pyrosetta | ACES FASTER |
Documentation, Uses, and more | ||||
| pysam | ACES FASTER |
Pysam is a Python module that provides access to read, write, manipulate, and analyze SAM/BAM files used in bioinformatics. It allows seamless integration of SAMtools, a set of utilities for interacting with and post-processing short DNA sequence read alignments in SAM, BAM, or CRAM format. | Bioinformatics, Sequence Analysis, Sam/Bam Files, Python Module | Biological Sciences | Library | Documentation, Uses, and more |
| pyscaf | FASTER | Documentation, Uses, and more | ||||
| pyseer | FASTER | Documentation, Uses, and more | ||||
| pyspoa | FASTER | PySpoa is a Python library for partial-order alignment (POA) that provides tools for performing accurate sequence alignment. Based on a divide-and-conquer strategy, PySpoa efficiently aligns sequences without global constraint and is especially useful for long read sequences in bioinformatics applications. | Bioinformatics, Sequence Alignment, Partial-Order Alignment, Python Library | Bioinformatics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| pystan | FASTER | PyStan is the Python interface for Stan, a probabilistic programming language for Bayesian statistical inference. PyStan allows users to define Bayesian models in Stan language and perform Bayesian analysis using Markov chain Monte Carlo (MCMC) methods. | Bayesian Statistics, Probabilistic Programming, Mcmc Methods, Statistical Inference | Statistics & Probability, Mathematics | Library | Documentation, Uses, and more |
| pytables | FASTER | Documentation, Uses, and more | ||||
| pytensor | ACES | PyTensor is a Python library for tensor operations and computations. It provides a high-level interface for handling multi-dimensional arrays and performing various tensor manipulations. | Python Library, Tensor Operations, Scientific Computing | Computer & Information Sciences | Scientific Computing | Documentation, Uses, and more |
| pytesseract | ACES | Pytesseract is a Python wrapper for Google's Tesseract-OCR Engine. It allows for easy integration of Tesseract OCR functionality in Python scripts. | Ocr, Text Recognition, Image Processing | Computer & Information Sciences | Ocr Library | Documentation, Uses, and more |
| pytest | ACES FASTER |
Pytest is a testing framework that makes it easy to write simple and scalable tests in Python. It is a popular testing framework used for testing Python programs and libraries. | Testing, Python, Framework | Computer & Information Sciences | Testing Framework | Documentation, Uses, and more |
| pytest-flakefinder | ACES FASTER |
pytest-flakefinder is a Pytest plugin that helps in detecting flaky tests by running them multiple times and analyzing the results. It identifies tests that fail intermittently due to non-deterministic behavior. | Pytest Plugin, Test Automation, Flaky Test Detection | Software Engineering, Systems & Development, Engineering & Technology | Plugin | Documentation, Uses, and more |
| pytest-rerunfailures | ACES FASTER |
pytest-rerunfailures is a plugin for the pytest testing framework that automatically reruns failed test cases to improve test reliability. | Software Testing, Python Libraries, Programming Tools | Software Engineering, Systems & Development, Engineering & Technology | Library | Documentation, Uses, and more |
| pytest-shard | ACES FASTER |
pytest-shard is a pytest plugin that allows test execution to be split across multiple workers for faster test runs. It enables parallel test execution by distributing the test load among several processes. | Pytest, Testing, Parallelization | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pytest-xdist | ACES FASTER |
pytest-xdist is a plugin for pytest that extends it with distributed testing capabilities. It allows for parallel execution of tests across multiple CPUs on the same machine or multiple machines, potentially reducing the overall test suite execution time. | Pytest, Testing, Distributed Computing, Parallel Execution | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pythia | ACES FASTER |
Pythia is a software package for event generation for high-energy collisions, implementing a number of hard scattering models for hadron collisions. It is commonly used in theoretical physics and high-energy physics research. | Event Generation, High-Energy Collisions, Theoretical Physics, Particle Physics | Particle & High-Energy Physics, Physical Sciences | Scientific Software | Documentation, Uses, and more |
| python | ACES Anvil Bridges-2 Delta DeltaAI FASTER KyRIC Ookami |
Python is a high-level, interpreted programming language known for its simplicity and readability. It supports multiple programming paradigms and has a vast ecosystem of libraries and frameworks. | Programming Language, Interpreted Language, High-Level Language | Computer & Information Sciences, Software Engineering, Systems & Development | Language | Documentation, Uses, and more |
| python-bundle-pypi | ACES FASTER |
Python-bundle-pypi is a collection of Python package bundles available on the Python Package Index (PyPI). These bundles consist of multiple Python libraries and utilities grouped together for convenience in installation and usage. | Python, Package, Pypi, Library, Utilities | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| python-igraph | FASTER | Documentation, Uses, and more | ||||
| python-isal | ACES FASTER |
Python bindings for Intel Storage Acceleration Library (ISAL) that provides optimized functions for storage protocols and data transformation. | Python Library, Data Transformation, Storage Protocols | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| python-parasail | FASTER | python-parasail is a Python library providing fast implementations of sequence alignment algorithms. It offers optimized implementations of pairwise sequence alignment based on the Parasail C library. | Sequence Alignment, Bioinformatics, Computational Biology, Python Library | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| python-venv | DeltaAI | Documentation, Uses, and more | ||||
| python/jax | Delta | Documentation, Uses, and more | ||||
| python/keras | Delta | Documentation, Uses, and more | ||||
| python/miniforge3_datascience | DeltaAI | Documentation, Uses, and more | ||||
| python/miniforge3_pytorch | Delta DeltaAI |
Documentation, Uses, and more | ||||
| python/miniforge3_tensorflow_cpu | DeltaAI | Documentation, Uses, and more | ||||
| python/miniforge3_tensorflow_cuda | DeltaAI | Documentation, Uses, and more | ||||
| python/pytorch | Delta | Documentation, Uses, and more | ||||
| python/scikit-learn | Delta | Documentation, Uses, and more | ||||
| python/tensorboard | Delta | Documentation, Uses, and more | ||||
| python/tensorflow | Delta | Documentation, Uses, and more | ||||
| python/torchaudio | Delta | Documentation, Uses, and more | ||||
| python/torchvision | Delta | Documentation, Uses, and more | ||||
| python3 | Expanse Ookami Stampede3 |
Python3 is a versatile, high-level programming language that is known for its readability and simplicity. It supports multiple programming paradigms such as object-oriented, imperative, functional, and procedural programming. Python3 has a comprehensive standard library and a large ecosystem of third-party packages, making it suitable for a wide range of applications. | Programming Language, Scripting Language | Computer & Information Sciences, Computer Science, Other Computer & Information Sciences | Interpreter | Documentation, Uses, and more |
| python37 | Expanse Ookami |
Python is an interpreted, interactive, object-oriented programming language. It incorporates modules, exceptions, dynamic typing, very high level dynamic data types, and classes. It supports multiple programming paradigms beyond object-oriented programming, such as procedural and functional programming. Python combines remarkable power with very clear syntax. It has interfaces to many system calls and libraries, as well as to various window systems, and is extensible in C or C++. It is also usable as an extension language for applications that need a programmable interface. Finally, Python is portable: it runs on many Unix variants including Linux and macOS, and on Windows. Description Source: https://docs.python.org/3/faq/general.html#what-is-python |
Documentation, Uses, and more | |||
| python_cacher | Stampede3 | python_cacher is a Python package for caching function results and improving computational efficiency by storing and retrieving expensive function calls. | Python Library, Function Caching, Computational Efficiency | Computer & Information Sciences | Library | Documentation, Uses, and more |
| pytorch | ACES Anvil Bridges-2 Delta FASTER Ookami |
PyTorch is an open-source machine learning library used for numerical computations and building deep learning models. | Machine Learning, Deep Learning, Numerical Computation, Neural Networks | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| pytorch-bundle | ACES FASTER |
Documentation, Uses, and more | ||||
| pytorch-geometric | ACES FASTER |
PyG (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data. Description Source: https://github.com/pyg-team/pytorch_geometric |
Python Library | Documentation, Uses, and more | ||
| pytorch-lightning | ACES FASTER |
PyTorch Lightning is the deep learning framework for professional AI researchers and machine learning engineers who need maximal flexibility without sacrificing performance at scale. Lightning evolves with you as your projects go from idea to paper/production. Description Source: https://lightning.ai/docs/pytorch/stable/ |
Python Library | Documentation, Uses, and more | ||
| pytorch3d | FASTER | PyTorch3D is a library for deep learning with 3D data, offering a modular and efficient differentiable rendering pipeline for 3D computational geometry deep learning research. It provides a variety of high-performance, modular components for 3D computer vision and graphics tasks. | Deep Learning, 3D Data, Computer Vision, Graphics, Modular Components | Computer Science, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| pyvcf | FASTER | Documentation, Uses, and more | ||||
| pywgcna | FASTER | Documentation, Uses, and more | ||||
| pyyaml | ACES FASTER |
PyYAML is a YAML parser and emitter for Python. It supports YAML 1.2 specification and can parse and emit YAML data quickly and efficiently. | Yaml, Parser, Emitter | Other Computer & Information Sciences, Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| pyzmq | ACES FASTER |
PyZMQ is a Python library that provides bindings for ZeroMQ. ZeroMQ is a high-performance asynchronous messaging library that allows you to build distributed applications. | Python Library, Messaging Library, Distributed Applications, Asynchronous Messaging | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| qca | ACES FASTER |
QCA (Qualitative Comparative Analysis) is a comparative analytical method primarily used in the social sciences to analyze data sets involving categorical variables. It is a method for studying the relationships between the presence and absence of conditions and an outcome of interest. | Qualitative Data Analysis, Comparative Analysis, Social Sciences | Social Sciences | Analytical Software | Documentation, Uses, and more |
| qcat | FASTER | QCAT is a software tool for managing and analyzing qualitative data. It is specifically designed to assist researchers in the coding, categorizing, and organizing of qualitative data such as text, images, audio, and video files. | Qualitative Data Analysis, Data Management, Research Tool | Social Sciences | Research Tool | Documentation, Uses, and more |
| qchem | FASTER Stampede3 |
Q-Chem is an ab initio quantum chemistry software package for fast and accurate simulations of molecular systems, including electronic and molecular structure, reactivities, properties, and structure. Description Source: https://www.q-chem.com/ |
Chemistry | Documentation, Uses, and more | ||
| qd | Ookami | qd is a library for fast computation of numerical quaternion and dual numbers. It provides tools for arithmetic operations, calculus, and linear algebra with quaternions and dual numbers. | Library, Numerical Computation, Quaternions, Dual Numbers | Mathematics | Library | Documentation, Uses, and more |
| qemu | ACES Anvil |
QEMU is a generic and open-source machine emulator and virtualizer that supports executing different operating systems and programs on a host operating system. It provides full system simulation, allowing users to run virtual machines with various architectures (x86, ARM, PowerPC, etc.) on a wide range of host platforms. QEMU can be used for various purposes such as development, testing, debugging, and virtualization. | Virtualization, Emulation, System Development | Biology, Computer & Information Sciences | Virtual Machine Emulator | Documentation, Uses, and more |
| qgis | ACES Anvil FASTER |
QGIS is a free and open-source cross-platform desktop geographic information system (GIS) application that supports viewing, editing, and analysis of geospatial data. | Gis, Mapping, Geospatial, Open Source | Earth & Environmental Sciences | Geo-Spatial Software | Documentation, Uses, and more |
| qhull | ACES FASTER |
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. | Computational Geometry, Libraries, Mesh Generation, Geometry Processing | Other Mathematics | Libraries | Documentation, Uses, and more |
| qiime2 | ACES FASTER |
QIIME 2â„¢ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. Description Source: https://qiime2.org/ |
Biology | Documentation, Uses, and more | ||
| qiskit | FASTER | Documentation, Uses, and more | ||||
| qiskit-aer | Delta | Documentation, Uses, and more | ||||
| qjson | ACES | QJson is a Qt-based library that maps JSON data to QVariant objects. It allows for easy JSON serialization and deserialization in Qt applications. | Json, Qt, Serialization, Deserialization | Computer & Information Sciences | Serialization/Deserialization | Documentation, Uses, and more |
| qrupdate | FASTER | qrupdate is a Python library for updating and solving the QR factorization. It provides functions to update a QR factorization of a matrix when new columns are added, as well as solving linear least squares problems based on the updated QR factorization. | Python Library, Qr Factorization, Linear Least Squares, Math Library | Mathematics | Mathematical Computing | Documentation, Uses, and more |
| qscintilla | ACES FASTER |
QScintilla is a port to Qt of Neil Hodgson's Scintilla editing component. It provides a rich text editing features and is commonly used for source code editing in integrated development environments (IDEs) and text editors. | Text Editing, Source Code Editing, Ides | Engineering & Technology | Text Editor | Documentation, Uses, and more |
| qt | Anvil | Qt is a cross-platform C++ framework for application development. It provides a comprehensive set of libraries and tools for building graphical user interfaces, as well as for developing applications with network support, database integration, and more. | C++ Framework, Application Development, Cross-Platform, Graphical User Interface, Network Programming, Database Integration | Engineering & Technology | Framework | Documentation, Uses, and more |
| qt5 | ACES FASTER |
Qt is a comprehensive cross-platform C++ application framework that is widely used for developing application software with a graphical user interface (GUI), and also used for developing non-GUI programs such as command-line tools and consoles for servers. It allows developers to write code once and deploy it across various desktop, mobile, and embedded operating systems without rewriting the codebase. Qt5 is the latest version of the Qt development framework. | Software Development, Cross-Platform, Gui Development, C++ Framework | Engineering & Technology | Application Development | Documentation, Uses, and more |
| qt5webkit | ACES FASTER |
Qt 5 Webkit is a module for the Qt 5 framework that allows developers to integrate web content into their applications. It provides a web rendering engine based on the open-source WebKit engine, allowing Qt applications to display and interact with web content. | Web Content Integration, Ui Development, Qt Framework | Computer Science, Computer & Information Sciences | Library | Documentation, Uses, and more |
| qt6 | FASTER | Documentation, Uses, and more | ||||
| qtconsole | FASTER | Documentation, Uses, and more | ||||
| qtkeychain | ACES FASTER |
QtKeychain is a Qt API to store passwords securely | Password Management, Security | Documentation, Uses, and more | ||
| qtpy | FASTER | Documentation, Uses, and more | ||||
| qualimap | FASTER | QualiMap is a quality control tool for high-throughput sequencing data. It provides a user-friendly interface to assess the quality of sequencing data generated by platforms such as Illumina, Roche 454, and Ion Torrent. QualiMap offers both basic and advanced quality metrics to help researchers evaluate the accuracy and reliability of their sequencing data. | Quality Control, High-Throughput Sequencing, Data Analysis | Bioinformatics, Biological Sciences | Quality Control Tool | Documentation, Uses, and more |
| quantum espresso | Stampede3 | Documentation, Uses, and more | ||||
| quantum-espresso | Anvil Ookami |
Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Description Source: https://www.quantum-espresso.org/ |
Chemistry | Package | Documentation, Uses, and more | |
| quantum_espresso | Anvil | Documentation, Uses, and more | ||||
| quantumespresso | ACES Bridges-2 FASTER Ookami |
Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. Description Source: https://www.quantum-espresso.org/ |
Chemistry | Package | Documentation, Uses, and more | |
| quast | ACES FASTER |
QUAST (Quality Assessment Tool for Genome Assemblies) is a software tool used for evaluating and comparing genome assemblies. It generates various metrics and statistics to assess the quality and accuracy of genomic assemblies. | Genome Assembly, Bioinformatics, Quality Assessment | Genomics, Biological Sciences | Stand-Alone Tool | Documentation, Uses, and more |
| quda | ACES | Documentation, Uses, and more | ||||
| quicktree | FASTER | Documentation, Uses, and more | ||||
| qupath | Bridges-2 | Documentation, Uses, and more | ||||
| qwt | ACES FASTER |
Qwt is a robust library for developing Qt applications that require 2D plotting and data visualization. It provides a set of classes and functions for creating various types of plots and graphs with different customization options. | 2D Plotting, Data Visualization, Qt Applications | Engineering & Technology | Libraries | Documentation, Uses, and more |
| r | ACES Anvil Delta DeltaAI FASTER Jetstream2 KyRIC Ookami |
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows, and MacOS. | Statistical Computing, Data Analysis, Statistical Graphics | Biostatistics, Medical & Health Sciences | Statistical Software | Documentation, Uses, and more |
| r-bundle-bioconductor | ACES FASTER |
Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. | Documentation, Uses, and more | |||
| r-bundle-cran | ACES FASTER |
Documentation, Uses, and more | ||||
| r-rmpi | FASTER | Documentation, Uses, and more | ||||
| r_flexiblas | Delta | r_flexiblas is a software package for solving linear systems with block-angular structures. It is based on the pre-conditioned flexible GMRES iterative solver combined with a block-ILU(0) pre-conditioner. The software is written in R and primarily designed for efficient solution of large, sparse linear systems arising from computational simulations in various scientific and engineering disciplines. | Linear Systems Solver, Computational Mathematics, Iterative Methods, Sparse Linear Systems | Applied Mathematics, Mathematics | Linear Algebra Library | Documentation, Uses, and more |
| r_tamu | ACES FASTER |
r_tamu is a simulation software for thermal and mechanical unit operations in chemical engineering. | Simulation Software, Chemical Engineering, Thermal Unit Operations, Mechanical Unit Operations | Chemical Engineering, Engineering & Technology | Engineering & Technology | Documentation, Uses, and more |
| racon | ACES FASTER |
Racon is a consensus module for correcting errors in long reads generated by third-generation sequencing technologies. It utilizes both a partially ordered de Bruijn graph and a fuzzy pairwise aligner to achieve high accuracy error correction. | Bioinformatics, Sequence Analysis, Genomics | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ragel | FASTER | Ragel is a domain-specific language and state machine compiler used for creating efficient state machine code in various programming languages. It can be employed for parsing, scanning, and code generation tasks. | State Machine Compiler, Domain-Specific Language, Code Generation, Parsing, Compilers | Other Computer & Information Sciences, Computer & Information Sciences | Domain-Specific Language | Documentation, Uses, and more |
| ragtag | FASTER | RagTag is a software tool designed to scaffold, polish, and evaluate assemblies by aligning them to reference genomes. It is particularly useful for improving the quality of genome assemblies and identifying misassemblies. | Assembly Improvement, Genome Alignment, Assembly Evaluation | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| rapidjson | ACES FASTER |
RapidJSON is a fast JSON parser and generator for C++ with both SAX/DOM styles. It is designed to be highly memory efficient and is self-contained with no external dependencies. | Json, C++, Parser, Generator, Sax, Dom, Memory Efficient | Computer & Information Sciences | Library | Documentation, Uses, and more |
| rapids | ACES | RAPIDS is a suite of open-source software libraries and APIs built on NVIDIA CUDA for executing end-to-end data science and analytics pipelines entirely on GPUs. It allows for faster processing and analysis of big data. | Data Science, Analytics, Gpu Computing | Computer & Information Sciences | Data Science | Documentation, Uses, and more |
| rapidsai | Anvil | RAPIDS is a collection of open source software libraries and APIs that gives you the ability to execute end-to-end data science and analytics pipelines entirely on NVIDIA GPUs using familiar PyData APIs. Description Source: https://rapids.ai/learn-more/#about |
Documentation, Uses, and more | |||
| rapsearch2 | ACES FASTER |
Documentation, Uses, and more | ||||
| raspa2 | FASTER | Documentation, Uses, and more | ||||
| rasterio | ACES FASTER |
Rasterio is a Python library for reading and writing geospatial raster datasets. It is built on the capabilities of the GDAL (Geospatial Data Abstraction Library) and provides easy access to the functionalities for opening, reading, and writing geospatial raster data formats. | Python Library, Geospatial Data, Raster Data, Gdal, Remote Sensing | Earth & Environmental Sciences | Data Processing/Analysis | Documentation, Uses, and more |
| raven | ACES | Documentation, Uses, and more | ||||
| raxml | Bridges-2 FASTER |
RAxML (Randomized Axelerated Maximum Likelihood) is a software for phylogenetic analysis and inference of evolutionary trees. It is widely used for maximum likelihood-based phylogenetic tree estimation. | Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| raxml-ng | FASTER | RAxML-NG (RAxML Next Generation) is a fast and accurate phylogenetic inference tool that implements maximum likelihood methods for large-scale phylogenetic tree estimation. It is designed to efficiently analyze large datasets with thousands of taxa and can handle diverse types of evolutionary models. | Phylogenetics, Evolutionary Biology, Bioinformatics | Systematics & Population Biology, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| ray-project | ACES FASTER |
Ray is a fast and simple framework for building and running distributed applications. | Documentation, Uses, and more | |||
| rclone | Bridges-2 Expanse FASTER Ookami |
Rclone is a command-line program to manage files on cloud storage. It is a powerful tool that supports various cloud storage services and allows users to sync files between different storage locations. | Cloud Storage, File Synchronization, Command-Line Tool | Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| rdflib | ACES FASTER |
RDFLib is a Python library for working with RDF (Resource Description Framework) data. It allows users to create, parse, modify, serialize, and query RDF graphs. | Rdf, Python Library | Computer & Information Sciences | Data Management | Documentation, Uses, and more |
| rdkit | ACES FASTER |
RDKit is an open-source toolkit for cheminformatics that provides a wide range of functionality for cheminformatics, including molecular modeling, cheminformatics, and machine learning tools. | Cheminformatics, Molecular Modeling, Cheminformatics Toolkit | Chemical Sciences, Natural Sciences | Toolkit | Documentation, Uses, and more |
| re2 | ACES FASTER |
RE2 is a fast, safe, thread-friendly, and efficient regular expression library. It provides better performance than many widely used regular expression libraries by using automata theory, generating linear-time matching algorithms. | Regular Expression, Library, Performance, Thread-Safe | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| re2c | ACES DeltaAI FASTER |
re2c is a tool for writing fast and flexible lexer/scanner programs. It translates regular expressions into deterministic finite automata (DFA) and compiles them into C/C++ code. This allows for efficient lexical analysis of input streams. | Lexer, Scanner, Regular Expressions, Dfa | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| readline | Anvil Delta DeltaAI KyRIC Ookami |
GNU Readline is a free software library that provides line-editing and history capabilities for interactive programs with a command-line interface. It allows users to edit command lines as they are typed in, recall and re-edit previous input, and perform basic character manipulations. | Gnu, Command Line Interface, Interactive Programs, Line Editing, History Manipulation | Computer & Information Sciences | Command Line Tool | Documentation, Uses, and more |
| readline-devel | Ookami | The readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The default editing mode is Emacs, but this can be changed when the application is run. In Emacs mode, the command line can be edited using the standard Emacs keystrokes. | Software Development, Library, Command Line Editing | Engineering & Technology | Development | Documentation, Uses, and more |
| recon | FASTER | Documentation, Uses, and more | ||||
| redis | ACES FASTER |
Redis is an open-source, in-memory data structure store that can be used as a database, cache, and message broker. It supports various data structures such as strings, hashes, lists, sets, sorted sets with range queries, bitmaps, hyperloglogs, geospatial indexes with radius queries, and streams. | Database, Cache, Message Broker | Computer & Information Sciences | Data Store | Documentation, Uses, and more |
| redis-py | ACES FASTER |
redis-py is a Python client library for Redis, a popular in-memory data store. It allows Python developers to easily interact with a Redis database to store and retrieve data. | Python Library, Database Interaction, In-Memory Data Store, Data Persistence | Computer & Information Sciences | Client Library | Documentation, Uses, and more |
| reframe | ACES | ReFrame is a Python library for writing tests for High Performance Computing (HPC) systems. It provides a functional testing framework designed to support a variety of different HPC systems. | Hpc, Python Library, Testing Framework | Engineering & Technology | Software Development | Documentation, Uses, and more |
| relion | Anvil FASTER |
Relion is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). | Cryo-Em, Image Processing, 3D Reconstruction, Macromolecular Complexes | Bioinformatics, Biological Sciences | Image Processing | Documentation, Uses, and more |
| remora | Stampede3 | Remora is a lightweight and extensible Python library for parallel and distributed computing workflows. It simplifies the process of distributing tasks across multiple workers and managing dependencies in a distributed environment. | Python Library, Parallel Computing, Distributed Computing | Computer & Information Sciences | Parallel & Distributed Computing | Documentation, Uses, and more |
| renderproto | Anvil | Documentation, Uses, and more | ||||
| repeatmasker | FASTER | RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. It can be used to identify repetitive elements, such as transposons and retroviruses, in genomic sequences. | Genomics, Bioinformatics, Sequence Analysis, Repeat Detection | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| repeatmodeler | FASTER | RepeatModeler is a tool for de novo identification, classification, and analysis of repetitive elements in genomic sequences. It combines several software packages and custom Perl scripts to build consensus models of repeat families from repeat sequences present in a genome. | Genomics, Bioinformatics, Repeat Sequences, De Novo Identification | Bioinformatics, Biological Sciences | Research Tool | Documentation, Uses, and more |
| repeatscout | FASTER | RepeatScout is a computational tool designed for the identification and classification of repetitive sequences in genomic data. It utilizes de novo repeat detection algorithms to discover novel repetitive elements within DNA sequences. | Genomics, Bioinformatics, Computational Biology | Biological Sciences | Genomic Sequence Analysis | Documentation, Uses, and more |
| revbayes | FASTER | RevBayes is a probabilistic programming framework for Bayesian inference of phylogenetic trees and evolutionary parameters. | Phylogenetics, Bayesian Inference, Evolutionary Biology | Systematics & Population Biology, Biological Sciences | Probabilistic Programming Tool | Documentation, Uses, and more |
| rfdiffusion | FASTER | Documentation, Uses, and more | ||||
| rfdiffusionaa | FASTER | Documentation, Uses, and more | ||||
| ribodetector | FASTER | Documentation, Uses, and more | ||||
| rich-cli | Bridges-2 | Documentation, Uses, and more | ||||
| rioxarray | ACES FASTER |
rioxarray is a Python package that extends xarray to add geospatial capabilities by making use of rasterio for I/O operations with raster data. It enables reading and writing spatial raster data with ease and integrates seamlessly with xarray for analysis and manipulation of these geospatial datasets. | Python Library, Geospatial Data, Raster Data, Data Processing | Earth & Environmental Sciences | Python Package | Documentation, Uses, and more |
| rising | ACES | RISING (Rapidly Installed Systems Engineering) is an open-source systems engineering tool that focuses on automating the system development process. It provides a framework for designing, integrating, and verifying complex systems with an emphasis on modularity, reusability, and maintainability. | Systems Engineering, Automation, Modularity, Reusability, Maintainability | Software Engineering, Systems & Development, Engineering & Technology | Systems Engineering | Documentation, Uses, and more |
| rjags | FASTER | Documentation, Uses, and more | ||||
| rlwrap | FASTER | rlwrap is a readline wrapper that uses the GNU readline library to allow the editing of keyboard input for any command. It provides command history, persistent history, line editing, and tab completion capabilities for command line interfaces. | Command Line Interface, Readline, Line Editing, Tab Completion | Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| rmblast | FASTER | Documentation, Uses, and more | ||||
| rnalysis | FASTER | rnalysis is a Python library designed for the analysis of RNA sequencing data. It provides functions for processing and analyzing gene expression data obtained from RNA-Seq experiments. rnalysis simplifies the preprocessing, quality control, differential expression analysis, and visualization of RNA-Seq data. | Python Library, RNA Sequencing Data, Gene Expression Analysis, Data Visualization | Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| rnaquast | ACES FASTER |
RNAQuast is a quality assessment tool for de novo transcriptome assembly pipelines. It evaluates the quality of transcriptome assemblies by comparing them to a reference genome and measures various metrics to assess the completeness, correctness, and compatibility of the assembly. | Bioinformatics, Transcriptome Analysis, Quality Assessment, Genomics | Biological Sciences | Quality Assessment Tool | Documentation, Uses, and more |
| rnastructure | FASTER | Documentation, Uses, and more | ||||
| rnaview | Bridges-2 | RNAview is a software tool for visualizing RNA secondary structures. It provides an interactive graphical interface for users to explore and analyze RNA molecules' structural properties. | RNA Secondary Structure, Visualization Tool, Bioinformatics | Bioinformatics, Biological Sciences | Molecular Biology | Documentation, Uses, and more |
| roary | FASTER | Roary is a high-speed stand-alone tool for detecting core genes from prokaryotic pan-genomes. It is particularly useful for performing fast pan-genome analyses of thousands of prokaryotic genomes. | Bioinformatics, Genomics, Pan-Genome Analysis, Prokaryotic Genomes | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| rocksdb | FASTER | Documentation, Uses, and more | ||||
| rocm-cmake | FASTER | ROCm CMake is an open-source set of CMake modules designed to facilitate building software with the ROCm ecosystem. It provides CMake configurations and utilities to enable ROCm development and integration of HIP and HCC compilers into projects. | Rocm, Cmake, Hip Compiler, Hcc Compiler | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| rocm-compilersupport | FASTER | Documentation, Uses, and more | ||||
| rocm-smi | FASTER | rocm-smi is a command-line program that allows users to monitor and manage AMD Radeon Open Compute (ROCm) System Management Interface (SMI) enabled GPUs. It provides detailed information about the current state of the GPUs and enables users to manage various aspects of the GPUs such as power management, fan speed control, temperature monitoring, and more. | Gpu Management, Performance Monitoring, System Management Interface, Amd Radeon, Rocm | Engineering & Technology | Command-Line Interface | Documentation, Uses, and more |
| rocr-runtime | FASTER | The ROCR Runtime (ROCR) is a runtime system designed for GPU-accelerated computing using ROCm platforms. It provides a high-performance environment for executing applications on AMD GPUs for parallel processing tasks. | Gpu-Accelerated Computing, Parallel Processing, Amd Gpus | Computer & Information Sciences | High-Performance Computing | Documentation, Uses, and more |
| roct-thunk-interface | FASTER | The roct-thunk-interface is a component of the ROCm project that provides a thin abstraction layer for various ROCm tools and libraries to interact with the ROCr driver. | Rocm, Gpu, Abstraction Layer, Compatibility | Computer Science, Computer & Information Sciences | Interface | Documentation, Uses, and more |
| root | ACES FASTER |
ROOT is an open-source data analysis framework used by high-energy physics (HEP) experiments. It provides a range of tools for data manipulation, visualization, statistical analysis, and storage. ROOT is written in C++ and offers a scripting language called ROOT/CINT that allows for quick prototyping and interactive analysis. | Data Analysis, Visualization, High-Energy Physics, Data Manipulation, Statistical Analysis | Particle & High-Energy Physics, Physical Sciences | Library | Documentation, Uses, and more |
| rosetta | ACES FASTER |
Documentation, Uses, and more | ||||
| rpmrebuild | ACES FASTER |
Documentation, Uses, and more | ||||
| rpy2 | FASTER | Documentation, Uses, and more | ||||
| rsem | ACES FASTER |
RSEM (RNA-Seq by Expectation Maximization) is a software package for estimating gene and isoform expression levels from RNA-Seq data. It quantifies the abundances of transcripts by calculating maximum likelihood estimates based on the Expectation-Maximization algorithm. | RNA-Seq, Transcriptomics, Gene Expression, Bioinformatics | Genomics, Biological Sciences | Computational Tool | Documentation, Uses, and more |
| rseqc | FASTER | RSeQC provides a number of standalone modules to check quality of RNA-Seq experiments, from raw data to the final result. | RNA-Seq, Quality Control, Gene Expression Analysis | Biological Sciences | Tool | Documentation, Uses, and more |
| rstudio | Anvil Expanse Jetstream2 Ookami |
RStudio is an integrated development environment (IDE) for R, a programming language and environment widely used for statistical computing and graphics. RStudio provides an intuitive and productive user interface for R, allowing users to efficiently write, execute, and debug R code. | Ide, Statistical Computing, Data Visualization, Programming | Other Natural Sciences | Ide | Documentation, Uses, and more |
| rstudio_singularity | FASTER | Documentation, Uses, and more | ||||
| ruamel.yaml | ACES FASTER |
ruamel.yaml is a YAML 1.2 loader/dumper package for Python. It is a superset of the PyYAML library and it includes round-trip parsing (which allows for preserving comments and formatting when loading and then emitting the YAML data). | Yaml, Parser, Dumper, Python | Computer & Information Sciences | Data Serialization | Documentation, Uses, and more |
| ruby | ACES FASTER |
Ruby is a dynamic, object-oriented programming language focused on simplicity and productivity. It has an elegant syntax that is easy to read and write, making it a popular choice for web development and scripting. | Programming Language, Scripting Language, Web Development | Computer & Information Sciences | Programming | Documentation, Uses, and more |
| rust | ACES Delta FASTER Ookami |
Rust is a multi-paradigm system programming language focused on safety, speed, and concurrency. | Programming Language, System Programming, Concurrency | Computer & Information Sciences | Compiler | Documentation, Uses, and more |
| s-lang | FASTER | Documentation, Uses, and more | ||||
| safetensors | ACES FASTER |
Documentation, Uses, and more | ||||
| salmon | ACES Delta FASTER |
Salmon is a wicked-fast program to provide quantification of transcript expression from RNA-seq data. | RNA-Seq, Transcript Expression Quantification | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| sambamba | FASTER | Sambamba is a high-performance tool and library for working with SAM/BAM files. It provides efficient and parallel processing of SAM and BAM files for tasks such as sorting, merging, indexing, and querying, with a focus on speed and reduced memory footprint. | Sam/Bam Files, High-Performance Tool, Parallel Processing, Genomics | Biological Sciences | Computational Software | Documentation, Uses, and more |
| samblaster | FASTER | Samblaster is a tool designed to mark duplicates and obtain discordant and split read alignments from SAM, BAM, or CRAM files, leveraging information from the SAM flags to accurately categorize the alignment information. | Bioinformatics, Hpc Tools | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| samclip | FASTER | Samclip is a software for adapter trimming and mapping of sequencing reads for various NGS applications. | Ngs, Sequencing, Bioinformatics | Bioinformatics, Biological Sciences | Tool | Documentation, Uses, and more |
| samtools | ACES Anvil Bridges-2 Delta FASTER |
Samtools is a suite of programs for interacting with high-throughput sequencing data generated in sequence alignment/map (SAM) format, such as those produced by the Short Read Mapping (SHRiMP) or Burrows-Wheeler Aligner (BWA) aligners. It allows various operations on SAM/BAM files, including indexing, sorting, merging, and manipulating sequence alignments. | Sequence Analysis, Genomics, Bioinformatics | Bioinformatics, Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| sanitizers4hpc | Delta DeltaAI |
sanitizers4hpc is a toolset designed for detecting and removing memory errors and data races in high-performance computing (HPC) applications. It offers various sanitizers to enhance the reliability and performance of parallel programs. | Memory Errors, Data Races, Hpc Applications | Computer Science, Engineering & Technology | Tool | Documentation, Uses, and more |
| sanitytool | Stampede3 | Sanitytool is a software tool designed for ensuring the sanity and quality of software code by performing various checks and validations. It helps in identifying potential issues, bugs, and vulnerabilities in the codebase, ensuring a higher level of code quality and reliability. | Software Quality Assurance, Code Analysis, Automated Testing, Continuous Integration | Software Engineering, Systems & Development, Engineering & Technology | Quality Assurance Tool | Documentation, Uses, and more |
| sas | FASTER | Documentation, Uses, and more | ||||
| scafacos | ACES FASTER |
SCAFACOS (Single-Cell Analysis Framework for Assessing Clonal Outcomes of Signaling) is a computational tool designed for analyzing single-cell signaling data and inferring clonal outcomes in cellular systems. It is specifically tailored for studying cellular heterogeneity and clonal dynamics in response to signaling pathways. | Computational Tool, Single-Cell Analysis, Signaling Pathways, Clonal Dynamics | Cell Biology, Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| scalapack | ACES Bridges-2 FASTER Ookami |
ScaLAPACK (Scalable LAPACK) is a parallel version of LAPACK (Linear Algebra PACKage) for distributed memory machines. It is designed to efficiently solve large-scale problems in numerical linear algebra using parallelism. | Linear-Algebra, Numerical-Computing, Distributed-Computing, Parallel-Computing | Other, Physical Sciences | Library | Documentation, Uses, and more |
| scalasca | ACES KyRIC Ookami |
Scalasca is a software toolset for analyzing the performance behavior of parallel applications and specifically for identifying potential performance bottlenecks. It assists users in optimizing the performance of their parallel applications by providing scalable and usable performance data. | Performance Analysis, Parallel Applications, Performance Optimization, Mpi Applications, Visualization | Software Engineering, Systems & Development, Computer & Information Sciences | Performance Analysis Tool | Documentation, Uses, and more |
| scalene | ACES FASTER |
Documentation, Uses, and more | ||||
| scanpy | FASTER | Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It provides a wide range of functionalities for quality control, preprocessing, visualization, clustering, trajectory inference, differential expression testing, and integration with other omics data. | Single-Cell RNA Sequencing Analysis, Bioinformatics, Data Visualization, Machine Learning | Bioinformatics, Biological Sciences | Python Library | Documentation, Uses, and more |
| schrodinger | ACES FASTER |
Schrodinger is a leading provider of advanced molecular simulations and quantum chemistry software for Life Sciences and Materials Research. The software suite offers a wide range of tools for drug discovery and materials science applications. | Molecular Simulations, Quantum Chemistry, Drug Discovery, Materials Research | Documentation, Uses, and more | ||
| scikit-bio | ACES FASTER |
scikit-bio is a Python library for bioinformatics that provides tools for biological data manipulation, analysis, and visualization. It offers functionality for working with biological sequence data, phylogenetic trees, and related metadata. | Bioinformatics, Python Library, Biological Data Analysis, Sequence Analysis | Bioinformatics, Biological Sciences | Library | Documentation, Uses, and more |
| scikit-build | ACES FASTER |
Scikit-build is an improved build system generator for CPython C/C++/Fortran/Cython extensions. It provides better support for CMake and enables you to easily build Python packages containing C++, C, Fortran, or Cython code. | Python Library, Build System, Cmake Integration | Computer & Information Sciences | Library | Documentation, Uses, and more |
| scikit-build-core | ACES FASTER |
Documentation, Uses, and more | ||||
| scikit-cuda | ACES | scikit-cuda is a Python library that provides a Python interface to Nvidia's CUDA parallel computation API. It aims to make GPU programming more accessible to Python developers by providing GPU-accelerated linear algebra operations and other numerical algorithms. | Python Library, Gpu Programming, Numerical Algorithms, Linear Algebra, Cuda Api | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| scikit-fda | FASTER | scikit-fda is a Python library designed for Functional Data Analysis (FDA) in the context of Scikit-learn. It provides tools for data representation, visualization, preprocessing, and modeling with functional data. | Functional Data Analysis, Python Library, Data Analysis, Machine Learning | Statistics & Probability, Mathematics | Library | Documentation, Uses, and more |
| scikit-image | ACES FASTER |
scikit-image is an open-source image processing library for the Python programming language that is designed to work with NumPy arrays. It provides a collection of algorithms for image processing, segmentation, feature extraction, and more. | Image Processing, Python Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| scikit-learn | ACES FASTER |
Scikit-learn is a machine learning library for the Python programming language. It features various classification, regression, and clustering algorithms including support vector machines, random forests, gradient boosting, k-means, and DBSCAN, among others. Scikit-learn is designed to interoperate with the Python numerical and scientific libraries NumPy and SciPy. | Machine Learning, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Libraries | Documentation, Uses, and more |
| scikit-misc | FASTER | Documentation, Uses, and more | ||||
| scipy | FASTER | SciPy is an open-source Python library that is used for scientific and technical computing. It provides efficient algorithms for numerical integration, optimization, linear algebra, interpolation, and more. SciPy builds on NumPy arrays for high-performance array operations and adds modules for statistics, signal processing, image processing, and other scientific computing tasks. | Scientific Computing, Numerical Algorithms, Python Library, Data Analysis, Signal Processing | Computer & Information Sciences, Other Computer & Information Sciences | Python | Documentation, Uses, and more |
| scipy-bundle | ACES FASTER |
The scipy-bundle is a comprehensive collection of scientific computing tools built on top of the SciPy library. It includes a wide range of modules and packages for numerical processing, optimization, statistics, integration, interpolation, signal processing, and more. | Scientific Computing, Numerical Processing, Statistics, Optimization, Signal Processing | Computer & Information Sciences, Other Computer & Information Sciences | Scientific Computing | Documentation, Uses, and more |
| scipy_tamu | FASTER | scipy_tamu is a software library that provides various scientific computing tools and algorithms tailored for research and educational purposes. | Scientific Computing, Mathematical Functions, Numerical Routines, Optimization, Linear Algebra | Applied Mathematics, Mathematics | Scientific Computing | Documentation, Uses, and more |
| scnic | FASTER | scnic is a Python package designed for the analysis, visualization, and interpretation of single-cell data. | Single-Cell Analysis, Data Visualization, Bioinformatics, Python Library | Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| scoary | FASTER | Documentation, Uses, and more | ||||
| scons | ACES FASTER |
SCons is an open-source software construction tool implemented in Python. It is designed to replace traditional build tools like Make with a more powerful and flexible build system. | Build Tool, Software Construction, Automation, Python | Engineering & Technology | Build Tool | Documentation, Uses, and more |
| score-p | ACES | Score-P is a performance measurement infrastructure designed to analyze and optimize the performance of parallel and distributed applications. It provides a set of measurement and analysis tools to assess the performance, scalability, and behavior of parallel applications. | Software, Performance Measurement, Parallel Computing, Distributed Computing | Engineering & Technology | Tool | Documentation, Uses, and more |
| scorep | KyRIC | The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. Score-P supports analyzing C, C++ and Fortran applications that make use of multi processing (MPI, SHMEM), thread parallelism (OpenMP, PThreads) and accelerators (CUDA, OpenCL, OpenACC) and combinations. It works in combination with Periscope, Scalasca, Vampir, and Tau. Description Source: https://www.vi-hps.org/projects/score-p |
Documentation, Uses, and more | |||
| scotch | ACES FASTER Stampede3 |
Scotch is a software package and library for graph and mesh partitioning, ordering, and clustering. It is designed to efficiently distribute data and computations across distributed memory parallel computers. | Graph Partitioning, Mesh Partitioning, Parallel Computing, Distributed Memory | Software Engineering, Systems & Development, Computer & Information Sciences | Library | Documentation, Uses, and more |
| screed | FASTER | Documentation, Uses, and more | ||||
| scripts_for_gb | FASTER | Documentation, Uses, and more | ||||
| sdl2 | ACES FASTER |
Simple DirectMedia Layer is a cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D. It is used by video playback software, emulators, and popular games including Valve's Steam. | Development, Multimedia, Graphics, Input-Output | Engineering & Technology | Development | Documentation, Uses, and more |
| sdl2_image | ACES | Documentation, Uses, and more | ||||
| sdl2_mixer | ACES | Documentation, Uses, and more | ||||
| sdl2_ttf | ACES | Documentation, Uses, and more | ||||
| sdsc | Expanse | SDSC (San Diego Supercomputer Center) is an organized research unit of the University of California, San Diego that provides cyberinfrastructure resources and services to researchers in the fields of computational science, data analytics, bioinformatics, and more. SDSC supports a wide range of scientific disciplines by offering high-performance computing resources, data storage solutions, software tools, consulting services, and training programs. | Supercomputing, Research Support, Data Analytics, Cyberinfrastructure | Computer & Information Sciences, Other Computer & Information Sciences, Engineering & Technology, Other Engineering & Technologies, Training, Infrastructure & Instrumentation | Documentation, Uses, and more | |
| sdsl | FASTER | Documentation, Uses, and more | ||||
| sdsl-lite | ACES | Documentation, Uses, and more | ||||
| se3-transformer | FASTER | Documentation, Uses, and more | ||||
| seaborn | ACES FASTER |
Seaborn is a Python data visualization library based on matplotlib. It provides a high-level interface for creating attractive and informative statistical graphics. | Python Library, Data Visualization, Statistical Graphics | Computer & Information Sciences | Library | Documentation, Uses, and more |
| seaview | FASTER | Documentation, Uses, and more | ||||
| segmentation-models | FASTER | Segmentation Models is an open-source library for semantic segmentation models that provides pre-trained models, scripts, and modular API for building custom segmentation models. | Semantic Segmentation, Deep Learning, Computer Vision, Image Processing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| sentencepiece | ACES FASTER |
SentencePiece is an unsupervised text tokenizer and detokenizer mainly for Neural Network-based text generation systems where the vocabulary size greatly affects the model performance. | Text Tokenizer, Neural Network, Text Generation | Computer & Information Sciences | Library/Tool | Documentation, Uses, and more |
| sepp | ACES FASTER |
SEPP (Satz per Partial Parsimony) is a software tool for aligning short DNA reads to a reference alignment in phylogenetic studies. It employs a phylogenetic placement strategy to assign reads to the reference tree in a computationally efficient manner. | Phylogenetics, DNA Alignment, Phylogenetic Placement | Bioinformatics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| seqan | FASTER | Documentation, Uses, and more | ||||
| seqkit | FASTER | SeqKit is a cross-platform, ultrafast, and handy sequenced data manipulation toolkit. It allows users to quickly manipulate sequences in fasta/fastq format, including filtering, splitting, removing duplicates, converting formats, and extracting sequences. SeqKit is designed to be efficient and user-friendly for handling large-scale sequencing data. | Sequence Manipulation, Fasta, Fastq | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| seqlib | ACES FASTER |
Documentation, Uses, and more | ||||
| seqmap | FASTER | Documentation, Uses, and more | ||||
| seqtk | FASTER | Documentation, Uses, and more | ||||
| seqwish | FASTER | Documentation, Uses, and more | ||||
| serf | ACES FASTER |
Serf is a decentralized solution for cluster membership, failure detection, and orchestration. It is lightweight and highly available, providing a mechanism for event broadcasting and key/value storage. | Cluster Management, Orchestration, Decentralized System | Engineering & Technology | Documentation, Uses, and more | |
| settarg | ACES Bridges-2 Delta DeltaAI FASTER Stampede3 |
Settarg is a command-line utility designed for setting target specific optimizations in C/C++ compilers. It helps in specifying optimization flags tailored for a particular CPU architecture to improve performance. | Compilers, Optimization, Performance Enhancement, Command-Line Tool | Computer & Information Sciences | Command-Line Utility | Documentation, Uses, and more |
| setuptools | ACES FASTER |
Setuptools is a package development process library designed to facilitate packaging Python projects. It allows developers to specify project metadata, declare project dependencies, and create distributable packages that can be easily installed using the Python package manager, pip. | Python Packaging, Package Management, Dependency Management | Computer Science | Library | Documentation, Uses, and more |
| setuptools-rust | ACES FASTER |
Setuptools-Rust is a Python library that extends the Setuptools build system, allowing you to build and distribute Rust packages from Python projects seamlessly. It simplifies the integration of Rust code into Python projects, making cross-language development easier and more efficient. | Python Library, Build System, Rust Integration | Software Engineering, Systems & Development, Computer & Information Sciences | Plug-In/Extension | Documentation, Uses, and more |
| shadow | KyRIC | Shadow is a versatile network simulator that is designed with the aim of providing not only an efficient and scalable simulation framework but also powerful and flexible scripting engines to automate complex simulations. | Network Simulation, Scripting, Simulation Framework | Computer Science, Computer & Information Sciences | Network Simulator | Documentation, Uses, and more |
| shap | ACES FASTER |
SHAP (SHapley Additive exPlanations) is a unified approach to explain the output of any machine learning model. It connects game theory with local explanations, attributing the impact of each feature on a model's predictions. | Explainability, Interpretability, Machine Learning, Model Explanation | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| shapeit4 | FASTER | SHAPEIT4 is a fast and accurate method for haplotype phasing based on a haplotype model similar to that used in SHAPEIT2. It adopts a new exact fragment inference algorithm that scales linearly with the effective number of haplotypes, making it highly efficient for large cohorts. SHAPEIT4 also includes a novel model that captures long-range phasing information through a conditional random field. | Phasing, Haplotype, Genomics, Bioinformatics, Computational Biology | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| shapely | ACES FASTER |
Shapely is a Python library for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries. | Python Library, Geospatial Analysis, Geometric Objects | Geographic Information Science, Earth & Environmental Sciences | Python Library | Documentation, Uses, and more |
| shared | Expanse Ookami |
Shared is a cloud-based collaboration platform that allows users to share files, documents, and information with team members or external collaborators. It provides a centralized location for real-time collaboration, file storage, version control, and communication. | Collaboration Platform, Cloud-Based Software, File Sharing, Communication, Version Control | Other | Cloud-Based Platform | Documentation, Uses, and more |
| sibelia | FASTER | Documentation, Uses, and more | ||||
| siesta | Bridges-2 Ookami Stampede3 |
Siesta is a computer program that performs electronic structure calculations based on density-functional theory. It is especially designed for tight-binding and ab-initio calculations in materials science. | Electronic Structure Calculations, Density-Functional Theory, Materials Science | Condensed Matter Physics, Physical Sciences | Material Science | Documentation, Uses, and more |
| signalp | FASTER | Documentation, Uses, and more | ||||
| silo | Stampede3 | Documentation, Uses, and more | ||||
| singularity | KyRIC Ookami |
Singularity is an open-source container platform designed to create, run, and manage containers for scientific and high-performance computing (HPC) workloads. It focuses on providing secure and portable environments for researchers and developers. | Containerization, Scientific Computing, Hpc, Research | Computer & Information Sciences, Engineering & Technology | Platform | Documentation, Uses, and more |
| singularitypro | Expanse | SingularityPro is a container platform that allows users to create, deploy, and manage containers for high-performance computing (HPC) environments. It is designed to provide users with a flexible and scalable solution for running applications in isolated environments. | Container Platform, Hpc, High-Performance Computing | Engineering & Technology | Container Platform | Documentation, Uses, and more |
| sionlib | ACES FASTER KyRIC |
Sionlib is a library that provides an I/O interface for scientific data stored in self-describing Hierarchical Data Format (HDF5) files, often used in high-performance computing applications. It offers functionalities for reading and writing data, metadata management, and dataset manipulation, making it a valuable tool for handling complex scientific data structures. | I/O Interface, Scientific Data, Hdf5 Files | Documentation, Uses, and more | ||
| sip | FASTER | SIP is a collection of tools that makes it very easy to create Python bindings for C and C++ libraries. It was originally developed in 1998 to create PyQt, the Python bindings for the Qt toolkit, but can be used to create bindings for any C or C++ library. For example it is also used to generate wxPython, the Python bindings for wxWidgets. Description Source: https://github.com/conda-forge/sip-feedstock/blob/main/recipe/meta.yaml | Documentation, Uses, and more | |||
| siscone | FASTER | Documentation, Uses, and more | ||||
| sklearn | Ookami | Documentation, Uses, and more | ||||
| slepc | ACES FASTER |
SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems. | Eigenvalue Problems, Sparse Matrices, Parallel Computing | Other Mathematics | Numerical Computing | Documentation, Uses, and more |
| slicer | FASTER | Documentation, Uses, and more | ||||
| slurm | Ookami | Slurm is an open-source workload manager designed for Linux clusters of all sizes. It provides job scheduling, prioritization, and management capabilities to maximize the efficiency of cluster resources. | Workload Manager, Cluster Management, High-Performance Computing | Engineering & Technology | Workload Manager | Documentation, Uses, and more |
| slurm-env | Delta | slurm-env is a tool that helps manage environment variables for SLURM job scripts. SLURM, which stands for Simple Linux Utility for Resource Management, is an open-source job scheduler for Linux clusters. | Slurm, Job Scheduler, Environment Variables, Linux Clusters | Engineering & Technology | Utility Tool | Documentation, Uses, and more |
| slurm/expanse | Expanse | Documentation, Uses, and more | ||||
| smithwaterman | ACES FASTER |
Documentation, Uses, and more | ||||
| smrt-link | FASTER | Documentation, Uses, and more | ||||
| snakemake | FASTER | Snakemake is a workflow management system that aims to improve the reproducibility and traceability of computational workflows. It allows users to define workflows in a human-readable and Python-based domain-specific language. | Workflow Management, Reproducibility, Traceability, Bioinformatics, Computational Biology, Data Science | Other Computer & Information Sciences | Software | Documentation, Uses, and more |
| snap | FASTER | SNAP (Stanford Network Analysis Platform) is a general purpose, high-performance system for analysis and manipulation of large networks. | Network Analysis, Large Networks, Graph Algorithms | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| snap-hmm | FASTER | Documentation, Uses, and more | ||||
| snappy | ACES FASTER |
Snappy is a fast compressor/decompressor for big data. It aims for very high speeds and reasonable compression levels. Snappy is widely used in many large-scale data processing frameworks. | Compression, Big Data, Data Processing | Computer & Information Sciences | Data Processing Tool | Documentation, Uses, and more |
| snippy | FASTER | Snippy is a tool for rapid haploid variant calling and core genome alignments of bacterial isolates. | Haploid Variant Calling, Core Genome Alignments, Bacterial Isolates | Bioinformatics, Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| snp-sites | FASTER | snp-sites is a software tool used for identifying single nucleotide polymorphisms (SNPs) from a multi-FASTA alignment of DNA sequences. It extracts variable sites from the alignment and outputs the SNPs in various formats for downstream analysis. | Bioinformatics, Computational Biology, Genomics | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| snpeff | FASTER | SnpEff is a genetic variant annotation and functional effect prediction tool designed to annotate and predict the effects of genetic variants within genomic sequences. | Genetic Variants, Annotation, Functional Prediction | Biological Sciences | Tool | Documentation, Uses, and more |
| sox | ACES FASTER |
Documentation, Uses, and more | ||||
| spaceranger | FASTER | Space Ranger is a software package developed by 10x Genomics for analysis, visualization, and interpretation of spatially resolved transcriptomics data. It enables the processing of spatially resolved transcriptomics data generated using the 10x Genomics Visium platform. | Bioinformatics, Hpc Tools | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spack | ACES FASTER KyRIC Ookami |
Spack is a flexible package management tool designed to support multiple versions of software, compilers, libraries, and tools on a wide range of platforms and configurations. It helps users easily install, uninstall, and manage software and dependencies in a reproducible and customizable way. | Package Management, Software Installation, Dependency Management, Hpc, Scientific Computing | Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| spacy | ACES FASTER |
spaCy is a free, open-source library for advanced Natural Language Processing (NLP) in Python. It is designed with the goal of facilitating easy implementation of state-of-the-art NLP techniques. | Nlp, Natural Language Processing, Python Library | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Library | Documentation, Uses, and more |
| spades | ACES Bridges-2 FASTER |
SPAdes (St. Petersburg genome assembler) is a de novo genome assembly software tool designed for single-cell and multi-cell bacterial genome projects. It uses a combination of de Bruijn graph and mismatch correction algorithms to assemble highly accurate and contiguous draft genomes. | Genome Assembly, Bioinformatics, Computational Biology | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| spaln | FASTER | Documentation, Uses, and more | ||||
| spark | ACES Anvil Bridges-2 Delta Expanse FASTER |
Apache Spark is an open-source distributed computing system that provides an interface for programming entire clusters with implicit data parallelism and fault tolerance. | Distributed Computing, Big Data, Data Processing | Computer & Information Sciences | Distributed Computing System | Documentation, Uses, and more |
| sparsehash | ACES FASTER |
sparsehash is a C++ library that provides several hash-map implementations. These implementations are designed to be very space-efficient, but still allow fast lookups. | C++ Library, Hash-Map Implementations | Computer & Information Sciences | Data Structure | Documentation, Uses, and more |
| spdlog | Ookami | spdlog is a header-only, feature-rich, and highly performant logging library for C++ which provides various logging outputs and log levels. | Logging, C++, Performance | Computer & Information Sciences, Computer Science, Software Engineering, Systems & Development | Logging | Documentation, Uses, and more |
| spectra | FASTER | Documentation, Uses, and more | ||||
| speedseq | FASTER | SpeedSeq is a suite of open-source tools for rapidly analyzing sequencing data to identify infections. | Sequencing Data Analysis, Genetic Mutations, Infections | Biological Sciences | Computational Software | Documentation, Uses, and more |
| spfft | ACES | Documentation, Uses, and more | ||||
| spglib | ACES FASTER |
spglib is a software library for finding and manipulating the crystal symmetries written in C. It is primarily used for crystallography and solid-state physics research. | Crystallography, Solid-State Physics | Condensed Matter Physics, Physical Sciences | Computational Software | Documentation, Uses, and more |
| spglib-python | ACES FASTER |
Spglib-python is a Python wrapper for the C library Spglib, which is a library for finding and manipulating spacegroup symmetry. It provides a wide range of functionalities for crystallography and solid-state physics calculations. | Crystallography, Solid State Physics | Condensed Matter Physics, Physical Sciences | Python Library | Documentation, Uses, and more |
| spice-server | Anvil | Documentation, Uses, and more | ||||
| spine | FASTER | Documentation, Uses, and more | ||||
| spoa | FASTER | SPAdes Overlap-Layout-Consensus (SPOA) is a C++ library and command-line tool for sequence alignment using a partial order graph (POG). It provides an efficient way to align long error-prone reads (such as Nanopore or PacBio) by constructing a graph based on input sequences and then finding the optimal alignment through a dynamic programming algorithm. | Sequence Alignment, Bioinformatics, Long Reads, Graph Based Alignment | Bioinformatics, Biological Sciences | Command-Line Tool | Documentation, Uses, and more |
| spython | ACES FASTER |
Spython is a software tool that combines the functionalities of the Python programming language with specific features tailored for scientific computing, data analysis, and visualization tasks. It aims to streamline the workflow for researchers and scientists by providing an integrated environment for code development, data manipulation, and result visualization. | Scientific Computing, Data Analysis, Visualization, Python Programming, Research Tools | Computer & Information Sciences, Other Mathematics, Other Natural Sciences | Scientific Computing Tool | Documentation, Uses, and more |
| sqlalchemy | ACES FASTER |
Documentation, Uses, and more | ||||
| sqlite | ACES Anvil Delta DeltaAI FASTER KyRIC Stampede3 |
SQLite is a C-language library that implements a small, fast, self-contained, high-reliability, full-featured, SQL database engine. SQLite is the most widely deployed SQL database engine in the world. The source code for SQLite is in the public domain. | Relational Database, Sql, Database Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| squashfs | KyRIC | SquashFS is a compressed read-only filesystem for Linux. It enables efficient storage of files, in a compressed format, with a focus on high compression ratios. | Filesystem, Compression, Read-Only | Computer Science, Computer & Information Sciences | Filesystem | Documentation, Uses, and more |
| sra toolkit | Bridges-2 | Documentation, Uses, and more | ||||
| sra-toolkit | ACES FASTER |
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. Description Source: https://github.com/ncbi/sra-tools |
Biology | Documentation, Uses, and more | ||
| sra-tools | Delta | SRA-tools is a set of software tools developed by the National Center for Biotechnology Information (NCBI) to assist with the download and analysis of high-throughput sequencing data from the Sequence Read Archive (SRA). | Bioinformatics, Hpc Tools, Sequence Analysis, Data Processing, High-Throughput Sequencing | Bioinformatics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| sratoolkit | Anvil Expanse |
Biology | Documentation, Uses, and more | |||
| srprism | FASTER | Documentation, Uses, and more | ||||
| sspace_basic | FASTER | Documentation, Uses, and more | ||||
| sst-core | ACES FASTER |
Documentation, Uses, and more | ||||
| ssw | ACES FASTER |
Documentation, Uses, and more | ||||
| stacks | FASTER | Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. | Software, Computational Biology, Bioinformatics | Genomics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| staden | FASTER | Documentation, Uses, and more | ||||
| star | ACES Bridges-2 Delta FASTER |
STAR (Spliced Transcripts Alignment to a Reference) is a RNA-seq read aligner that maps RNA-seq data to a reference genome to identify splice junctions between exons. It is particularly useful for mapping reads that span multiple exons, thereby aiding in the analysis of alternative splicing events. | Software, RNA-Seq, Read Aligner, Splice Junctions, Alternative Splicing | Genetics, Biological Sciences | Alignment Tool | Documentation, Uses, and more |
| star-ccm+ | FASTER | Documentation, Uses, and more | ||||
| star-fusion | Bridges-2 | Star-Fusion is a computational tool developed to identify fusion transcripts from RNA-Seq data. It utilizes the STAR aligner to map reads and searches for evidence of chimeric transcripts, providing insight into gene fusions in cancer and other diseases. | RNA-Seq, Fusion Transcripts, Gene Fusions, Computational Tool | Bioinformatics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| starpu | ACES | StarPU is a runtime system designed for heterogeneous multicore machines with accelerators. It offers a unified runtime system that can handle multi-threading, task parallelism, data management, and data locality management. StarPU is specifically tailored for dense numerical linear algebra operation kernels and iterative solvers. | Runtime System, Heterogeneous Computing, Multicore Architectures | Other | Hpc Tool | Documentation, Uses, and more |
| stat | Delta DeltaAI |
Stat is a statistical software package designed for data analysis, statistical modeling, hypothesis testing, and visualization. | Statistics, Data Analysis, Statistical Modeling, Hypothesis Testing, Visualization | Mathematics | Data Analysis Tool | Documentation, Uses, and more |
| stata | FASTER | Stata is a statistical software package widely used by researchers in various disciplines for data analysis, data management, and visualization. It provides a comprehensive suite of statistical tools for both beginners and advanced users. | Statistical Software, Data Analysis, Data Management, Visualization | Statistics & Probability, Other Mathematics | Proprietary | Documentation, Uses, and more |
| statsmodels | ACES FASTER |
Statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. It also includes machine learning algorithms, such as clustering algorithms and supervised learning models. | Statistics, Data Analysis, Machine Learning, Python | Statistics & Probability | Data Analysis & Statistics | Documentation, Uses, and more |
| std_compat | FASTER | Documentation, Uses, and more | ||||
| stitch | FASTER | Documentation, Uses, and more | ||||
| stk | FASTER | Documentation, Uses, and more | ||||
| strace | ACES FASTER |
strace is a diagnostic, debugging and instructional userspace utility for Linux. It is used to monitor and tamper with interactions between processes and the Linux kernel, which include system calls, signal deliveries, and changes of process state. | Debugging, Diagnostic, Monitoring | Computer & Information Sciences | Diagnostic Tool | Documentation, Uses, and more |
| stringtie | Delta FASTER |
StringTie is a software for transcript assembly and quantification of RNA-Seq data. It is designed to efficiently assemble and quantify full-length transcripts representing multiple splice variants for each gene locus. | RNA-Seq, Transcript Assembly, Transcript Quantification | Biological Sciences | Transcriptomics Tool | Documentation, Uses, and more |
| structure | FASTER | Structure is a software package for using multi-locus genotype data to investigate population structure. Its main purpose is to assign individuals to populations, by analyzing multilocus genotype data. It can also be used to evaluate how well the data fit a particular number of populations, to help discover hierarchical population structure, to detect the presence of barriers to gene flow, and to identify migrants and hybrids. | Population Genetics, Population Structure, Genotype Analysis, Data Analysis | Ecology, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| strumpack | FASTER | STRUMPACK (STRUctured Matrices PACKage) is a software package for the compression, factorization, and solution of structured linear systems arising from various applications. It utilizes low-rank approximations and hierarchical matrices to efficiently handle large-scale structured linear systems. | Linear Algebra, Numerical Methods, Scientific Computing | Mathematics | Computational Software | Documentation, Uses, and more |
| subphaser | FASTER | Documentation, Uses, and more | ||||
| subread | FASTER | subread is a software package for processing next-generation sequencing data, including read mapping and quantification of gene and genomic feature expression levels. It is designed to efficiently handle large volumes of sequencing data with high accuracy and speed. | Ngs, Bioinformatics, Sequencing, Alignment | Bioinformatics, Biological Sciences | Ngs Analysis | Documentation, Uses, and more |
| subversion | ACES Delta Expanse FASTER |
Subversion (SVN) is an open-source version control system that allows users to manage files and directories, track changes in the source code, and collaborate with team members on software development projects. | Version Control, Software Development, Collaboration, Teamwork | Computer & Information Sciences | Development Tools | Documentation, Uses, and more |
| suitesparse | ACES FASTER Stampede3 |
SuiteSparse is a suite of sparse matrix algorithms and solvers available in the form of libraries that are designed to efficiently handle sparse matrices commonly encountered in numerical computations. | Sparse Matrix, Algorithms, Numerical Computations | Other Mathematics | Computational Software | Documentation, Uses, and more |
| sundials | ACES FASTER Stampede3 |
SUNDIALS (Suite of Nonlinear and Differential/Algebraic Equation Solvers) is a software package for the solution of large-scale, time-dependent nonlinear differential/algebraic systems. | Software, Numerical Integration, Differential Equations, Algebraic Equations, Scientific Computing | Other Mathematics | Library | Documentation, Uses, and more |
| superlu | ACES | SuperLU is a software package for solving large, sparse, nonsymmetric systems of linear equations on high-performance computers. It is based on the LU factorization with partial pivoting and triangular solution of the linear system. | Linear Algebra, Sparse Matrix, Direct Solver, Computational Science | Applied Mathematics, Mathematics | Solver Library | Documentation, Uses, and more |
| superlu_dist | ACES FASTER |
SuperLU_DIST is a parallel direct solver for large sparse systems of linear equations. It is designed for distributed memory parallel computers and can solve general, unsymmetric, linear systems Ax = b. | Linear Solver, Sparse Systems, Parallel Computing | Applied Mathematics, Mathematics | Library | Documentation, Uses, and more |
| svtyper | FASTER | svtyper is a tool designed to genotype structural variants. | Genotyping, Structural Variants, Whole-Genome Sequencing | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| swig | ACES Anvil DeltaAI FASTER Stampede3 |
SWIG (Simplified Wrapper and Interface Generator) is a software development tool that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, Tcl, and more. It simplifies the process of creating interfaces for these languages, enabling developers to easily incorporate C/C++ code into their scripting language-based projects. | Software Development, Programming Tool, Scripting Languages, Interface Generator | Computer & Information Sciences, Software Engineering, Systems & Development | Interface Generator | Documentation, Uses, and more |
| sylph | Ookami | Documentation, Uses, and more | ||||
| sympy | ACES FASTER |
SymPy is a Python library for symbolic mathematics that aims to become a full-featured computer algebra system. It provides capabilities for symbolic computation, algebraic manipulation, calculus, equation solving, and more. | Symbolic Mathematics, Computer Algebra System, Mathematics, Python Library | Pure Mathematics, Mathematics | Scientific Computing | Documentation, Uses, and more |
| synthcity | ACES | SynthCity is a software for urban simulation and modeling that allows researchers to simulate various aspects of urban environments and study the effects of different urban planning strategies. It provides a platform for detailed spatial analysis and scenario planning. | Urban Planning, Simulation Software, Spatial Analysis, Scenario Planning, Data Visualization | Library | Documentation, Uses, and more | |
| syri | FASTER | Syri is a software tool used for analyzing and visualizing complex networks and performing various network analysis tasks. It provides a wide range of functionalities for studying network structures and behaviors. | Network Analysis, Visualization, Complex Networks | Computer & Information Sciences | Network Analysis Tool | Documentation, Uses, and more |
| sz | FASTER Stampede3 |
Documentation, Uses, and more | ||||
| sz3 | FASTER | SZ3 is a high-performance data compression software designed for scientific data, with a focus on large-scale numerical simulations. It is optimized for compressing structured grid data commonly found in computational fluid dynamics and weather modeling applications. | Data Compression, Scientific Data, Numerical Simulations, Computational Science | Computer & Information Sciences | Documentation, Uses, and more | |
| szip | ACES FASTER |
szip is a compression tool specifically designed for scientific data sets. It is optimized for enhancing the performance of reading and writing data stored in the HDF5 file format by reducing the file size. szip uses a lossless compression algorithm to achieve data compression while maintaining data integrity. | Compression Tool, Scientific Data Sets, Hdf5 File Format | Other Natural Sciences, Engineering & Technology | Utility | Documentation, Uses, and more |
| tabixpp | ACES FASTER |
Documentation, Uses, and more | ||||
| tacc | Stampede3 | TACC (Texas Advanced Computing Center) provides comprehensive advanced computing resources and support services to researchers, enabling them to address some of society's most challenging problems. | High-Performance Computing, Advanced Computing Resources, Visualization, Data Analysis, Storage Solutions, Cloud Computing, Training, Education Programs | Infrastructure & Instrumentation, Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| tacc tips | Stampede3 | Documentation, Uses, and more | ||||
| taichi | FASTER | Taichi is a software infrastructure that enables preparing and running high-performance computation on parallel computing devices such as CPUs and GPUs. It focuses on providing a flexible and optimized framework for computational simulations and numerical methods. | Computational Software, Parallel Computing, Numerical Simulations | Engineering & Technology | Framework | Documentation, Uses, and more |
| tantan | FASTER | Documentation, Uses, and more | ||||
| tar | Anvil KyRIC |
tar is a software utility used for packaging files together into an archive file often referred to as a "tarball". It is commonly used in Unix-like operating systems for creating, storing, and managing files in a single file. | File Archiving, Compression, Terminal | Other, Computer & Information Sciences | File Management | Documentation, Uses, and more |
| tassel | FASTER | Tassel is a bioinformatics software tool used for analyzing genetic variation in plants. It provides a wide range of functionalities for genetic analysis, visualization, and data management, particularly designed for plant biologists and breeders. | Bioinformatics, Genetic Analysis, Plant Biology | Genetics, Biological Sciences | Analysis Tool | Documentation, Uses, and more |
| tau | KyRIC Ookami |
Tau is a performance analysis tool for parallel programs, providing insights into the behavior of applications across various HPC platforms. | Software, Compiler, Hpc Tools | Physical Sciences | Commercial | Documentation, Uses, and more |
| taxator-tk | FASTER | Documentation, Uses, and more | ||||
| tbb | ACES FASTER KyRIC |
Intel Threading Building Blocks (TBB) is a widely-used C++ template library for multicore programming that provides rich features for parallel programming. It offers a high-level abstraction for expressing parallelism to help developers create scalable, high-performance applications. | Multicore Programming, Parallel Computing, C++ Library, High Performance Computing | Computer & Information Sciences | Programming Library | Documentation, Uses, and more |
| tbb32 | KyRIC | Intel Threading Building Blocks (TBB) is a widely used C++ template library developed by Intel for parallel programming on multi-core processors. TBB provides higher-level abstractions for parallelism, making it easier to write code that can take advantage of multicore processors. | Parallel Programming, Multi-Core Processors, C++ Template Library, Intel | Computer & Information Sciences | Library | Documentation, Uses, and more |
| tbl2asn | ACES FASTER |
Documentation, Uses, and more | ||||
| tcl | ACES Anvil Delta Expanse FASTER |
Tool Command Language (Tcl) is a dynamic programming language often used for creating scripts, applications, and embedded control systems. It provides a simple scripting language and a powerful code execution environment for various platforms. | Scripting Language, Dynamic Programming Language, Cross-Platform, Scripting | Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tclap | FASTER | TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It is a mature, stable, lightweight, and efficient library for parsing command line arguments in C++ programs. | Command Line Arguments, Parsing, C++, Library | Engineering & Technology | Documentation, Uses, and more | |
| tcsh | ACES FASTER |
Tcsh is a command language interpreter that is based on and compatible with the C shell (csh). It offers extensive customization options and interactive features for command-line users. | Command-Line Interpreter, Shell Scripting, Unix-Like Operating Systems | Computer & Information Sciences | Language Interpreter | Documentation, Uses, and more |
| tdb | FASTER | Documentation, Uses, and more | ||||
| template | Ookami | Documentation, Uses, and more | ||||
| tensorboard | ACES FASTER |
TensorBoard is a suite of web applications for inspecting and understanding the TensorFlow runs and graphs. It enables visualization of TensorFlow graphs, as well as monitoring of training progress and evaluation metrics. | Tensorflow, Deep Learning, Visualization, Model Monitoring | Computer & Information Sciences | Web Application | Documentation, Uses, and more |
| tensorboardx | ACES FASTER |
TensorBoardX is a library for visualization and tracking of TensorFlow deep learning models. It enables visualization of training and testing processes, model graphs, scalar values, histograms, images, text, audio, and videos. It extends the functionality of TensorFlow's native TensorBoard with additional features and flexibility. | Visualization, Deep Learning, Tensorflow, Pytorch | Computer & Information Sciences | Library | Documentation, Uses, and more |
| tensorflow | ACES Anvil Bridges-2 Delta FASTER |
TensorFlow is an open-source machine learning library developed by Google to build and train deep learning models. | Machine Learning, Deep Learning, Neural Networks, Model Training | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning Framework | Documentation, Uses, and more |
| tensorflow-probability | ACES FASTER |
TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis. | Documentation, Uses, and more | |||
| tensorrt | ACES FASTER |
TensorRT is a high-performance deep learning inference optimizer and runtime for production deployment of deep learning applications. It maximizes runtime performance through optimizations like kernel fusion, layer fusion, and precision calibration. TensorRT also delivers low latency and high throughput for deep learning inference by leveraging GPU hardware. | Deep Learning Inference, Optimization, Gpu Acceleration, Production Deployment | Computer & Information Sciences | Runtime | Documentation, Uses, and more |
| tensorstore | ACES FASTER |
Documentation, Uses, and more | ||||
| termcap | FASTER | Documentation, Uses, and more | ||||
| tesmall | FASTER | Documentation, Uses, and more | ||||
| tesseract | ACES | Tesseract is an open-source OCR (Optical Character Recognition) engine that can be used to extract text from various sources like images, PDFs, and scanned documents. | Ocr, Text Recognition, Open-Source, Cross-Platform | Computer & Information Sciences | Ocr Tool | Documentation, Uses, and more |
| tetgen | FASTER | Documentation, Uses, and more | ||||
| texlive | ACES Anvil FASTER Ookami Stampede3 |
TeX Live is a comprehensive TeX and LaTeX distribution that provides an extensive collection of TeX-related programs, fonts, and macro packages. It offers a cross-platform TeX system for typesetting documents, mathematical formulas, publications, and other text-heavy content, widely used in academia, publishing, and science. | Documentation, Uses, and more | |||
| theano | ACES FASTER |
Theano is an open-source symbolic mathematical library, used for deep learning and numerical computation, that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. | Mathematical Library, Deep Learning, Numerical Computation | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Symbolic Mathematical Library | Documentation, Uses, and more |
| thermo-calc | FASTER | Thermo-Calc is a powerful software package for thermodynamic calculations and phase diagram calculations in materials science, metallurgy, and other related fields. It is widely used for studying phase equilibria, phase transformations, diffusion, and precipitation in multicomponent systems. | Materials Science, Metallurgy, Thermodynamics, Phase Equilibria, Phase Transformations | Metallurgical Engineering, Engineering & Technology | Computational Tool | Documentation, Uses, and more |
| tidk | FASTER | Documentation, Uses, and more | ||||
| tiger | Bridges-2 | TIGER (Topical Information in Genomic Experiments) is a software suite designed for the analysis and interpretation of genomics and transcriptomics data. It offers a range of tools for processing and visualizing genomic data to facilitate research in molecular biology and genetics. | Genomics, Transcriptomics, Data Analysis, Molecular Biology, Genetics | Genomics, Biological Sciences | Tool | Documentation, Uses, and more |
| tigmint | FASTER | Tigmint is a software tool that aids in the rearrangement and duplication error correction in genomes assembled with linked-read sequencing technologies such as 10X Genomics. | Genome Assembly, Genomics, DNA Sequencing, Linked-Read Sequencing | Genomics, Biological Sciences | Genome Assembly Correction Tool | Documentation, Uses, and more |
| time | ACES Delta FASTER |
Time is a fundamental quantity used to sequence and compare events. It is a concept which enables the measurement of durations and intervals, and forms the basis of various systems for measuring and quantifying changes. | Time, Measurement, Events, Synchronization | Other | Measurement & Timekeeping | Documentation, Uses, and more |
| tinker-hp | Delta | Tinker-HP is a molecular modeling software designed for high-performance simulations of biomolecular systems. It provides tools for molecular dynamics simulations, energy minimization, and analysis of complex biomolecular structures. | Molecular Modeling, Biomolecular Systems, Simulations | Biophysics, Biological Sciences | Molecular Dynamics Simulation Software | Documentation, Uses, and more |
| tk | ACES Anvil Delta FASTER |
Tkinter is a standard GUI toolkit for Python. It is included with most Python installations and is widely used for building desktop applications in Python. | Gui, Python, Toolkit, Desktop Applications | Computer & Information Sciences, Computer Science, Software Engineering, Systems & Development | Library | Documentation, Uses, and more |
| tkinter | ACES FASTER |
Tkinter is the standard GUI (Graphical User Interface) toolkit for Python. It provides a fast and easy way to create desktop applications with a collection of standard GUI elements. | Gui, Toolkit, Python Library | Computer & Information Sciences | Gui Toolkit | Documentation, Uses, and more |
| tmhmm | FASTER | Documentation, Uses, and more | ||||
| tmux | ACES | tmux is a terminal multiplexer that allows users to access multiple separate terminal sessions inside a single terminal window or remote shell. It enables users to switch easily between several programs in one terminal, detach them (leave them running in the background), and reattach them to a different terminal. | Terminal, Multiplexer, Session Management, Productivity | Computer & Information Sciences | Text-Based | Documentation, Uses, and more |
| toga | FASTER | Documentation, Uses, and more | ||||
| togl | FASTER | Documentation, Uses, and more | ||||
| tokenizers | ACES FASTER |
Documentation, Uses, and more | ||||
| tomli | FASTER | Tom's Obvious, Minimal Language (TOML) is a data serialization language designed to be a minimal configuration file format that's easy to read due to obvious semantics. TOML is designed to map unambiguously to a hash table. TOML files end with the .toml extension. | Toml, Configuration File Format, Data Serialization, Human-Readable, Machine-Readable | Software Engineering, Systems & Development, Computer & Information Sciences | Configuration File | Documentation, Uses, and more |
| tophat | Anvil | Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to the genome using the Bowtie aligner and then analyzes the mapping results to identify splice junctions between exons. | RNA-Seq, Splice Junction Mapper, Genomics | Biological Sciences | Genomic Analysis Tool | Documentation, Uses, and more |
| torch | FASTER | Documentation, Uses, and more | ||||
| torchani | Anvil | TorchANI is a PyTorch implementation of the ANI (Anisotropic Network Model) neural network potential for predicting molecular interactions and properties in chemical systems. | Computational Chemistry, Machine Learning, Python Library, Chemical Modeling | Physical Chemistry, Chemical Sciences | Python Library | Documentation, Uses, and more |
| torchinfo | FASTER | Torchinfo is a PyTorch library that provides detailed layer-by-layer model information, such as shapes, number of parameters, and memory usage. It helps in debugging neural network architectures and understanding the flow of data through the network. | Deep Learning, Neural Networks, Pytorch, Model Debugging | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Pytorch Library | Documentation, Uses, and more |
| torchsampler | ACES | torchsampler is a library for data sampling in PyTorch, designed to efficiently handle various sampling strategies and techniques to improve data processing and training of deep learning models. | Data Sampling, Pytorch, Deep Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Data Sampling | Documentation, Uses, and more |
| torchtext | ACES | torchtext is a library used for natural language processing (NLP) tasks in PyTorch. It provides utilities and datasets for processing text data, such as tokenization, vocabulary building, word embeddings, and data loading for NLP models. | Nlp, Natural Language Processing, Pytorch, Text Processing | Computer & Information Sciences | Library | Documentation, Uses, and more |
| torchvision | ACES FASTER |
Torchvision is a package in the PyTorch deep learning framework that consists of popular datasets, model architectures, and common image transformations for computer vision tasks. | Deep Learning, Computer Vision, Image Processing | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Deep Learning | Documentation, Uses, and more |
| tornado | ACES FASTER |
Tornado is a Python web framework and asynchronous networking library. It is designed for handling asynchronous processes and is commonly used for building web applications. | Python, Web Framework, Asynchronous, Networking | Computer & Information Sciences | Application Development | Documentation, Uses, and more |
| totalview | Anvil | TotalView is a comprehensive parallel debugging and performance analysis solution. It provides developers with advanced tools to effectively find and fix bugs, optimize code, and improve application performance for HPC, big data, and machine learning applications. | Debugging, Performance Analysis, Hpc, Big Data, Machine Learning | Infrastructure & Instrumentation, Engineering & Technology | Development & Optimization Tools | Documentation, Uses, and more |
| toxcodan-genome | FASTER | Documentation, Uses, and more | ||||
| tpmcalculator | FASTER | TPMCalculator is a computational tool that enables the quantification of gene expression levels from RNA-Seq data based on the transcripts per million (TPM) method. TPM calculations normalize read counts by the length of the transcripts and the total number of mapped reads, providing a more accurate representation of gene expression levels. | Bioinformatics, Computational Biology, RNA-Seq, Transcriptomics | Biological Sciences | Bioinformatics | Documentation, Uses, and more |
| tqdm | ACES FASTER |
tqdm is a fast, extensible progress bar for loops and pipelines in Python. It provides a visual and text-based progress bar to indicate the progress of iterations. | Progress Bar, Python, Data Visualization, Productivity Tool | Computer & Information Sciences | Package | Documentation, Uses, and more |
| transdecoder | ACES FASTER |
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or other full-length RNA-Seq datasets. It combines homology searches with open reading frame (ORF) detection to predict likely coding regions. | Bioinformatics, Computational Biology, Transcriptomics, Protein Prediction | Genetics, Biological Sciences | Tool | Documentation, Uses, and more |
| transformers | ACES FASTER |
Transformers is a state-of-the-art natural language processing library, which provides thousands of pre-trained models for various NLP tasks. It offers an easy-to-use API for training and fine-tuning models on custom datasets. | Nlp, Deep Learning, Machine Learning | Artificial Intelligence & Intelligent Systems, Computer & Information Sciences | Machine Learning | Documentation, Uses, and more |
| transrate | ACES | Transrate is a software tool for de novo transcriptome assembly quality analysis. It assesses the quality of de novo transcriptome assemblies, identifies problem areas, and suggests improvements. Transrate helps in evaluating the accuracy and completeness of transcriptome assemblies. | Transcriptome Assembly, Quality Assessment, Bioinformatics | Genetics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| treemix | FASTER | Documentation, Uses, and more | ||||
| trf | FASTER | Documentation, Uses, and more | ||||
| trilinos | ACES Stampede3 |
Trilinos is an open-source collection of solvers and libraries for the solution of large-scale, complex multi-physics engineering and scientific problems. It provides a framework for the development of parallel linear and nonlinear algebraic solvers, preconditioners, and other scientific computing capabilities. | Scientific Computing, Numerical Analysis, Parallel Computing, Computational Physics | Biology, Engineering & Technology | Library | Documentation, Uses, and more |
| trim_galore | ACES FASTER |
The TRIM (Thermal Radiation Interaction Model) software is used in computational fluid dynamics (CFD) simulations to accurately model thermal radiation exchanges within fluid flows. TRIM helps in studying the impact of thermal radiation on heat transfer and temperature distribution in various engineering applications. | Biology | Documentation, Uses, and more | ||
| trimal | FASTER | Trimal is a bioinformatics tool used for multiple sequence alignment trimming. It can remove poorly aligned positions or divergent regions in a sequence alignment, which can be beneficial for downstream phylogenetic analysis or evolutionary studies. Trimal offers several trimming methods and criteria to suit different research needs. | Bioinformatics, Sequence Analysis, Alignment Trimming | Bioinformatics, Biological Sciences | Alignment Trimming | Documentation, Uses, and more |
| trimmomatic | ACES Anvil Bridges-2 Delta FASTER |
Trimmomatic is a flexible and efficient tool for trimming raw next-generation sequencing data. It provides several trimming modes and options to cater to different sequencing platforms and quality control requirements. | Ngs Data Processing, Quality Control, Bioinformatics | Biology, Biological Sciences | Tool | Documentation, Uses, and more |
| trinity | ACES Bridges-2 FASTER |
Trinity is a de novo RNA-Seq assembly software that reconstructs transcriptomes from short RNA-Seq reads using a novel method for de novo transcriptome assembly from RNA-Seq data. It combines efficient full-length transcript assembly and full-length isoform reconstruction to result in high-sensitivity and high-accuracy transcriptomes. | Bioinformatics, Computational Biology, Transcriptomics, RNA-Seq, De Novo Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| trinotate | ACES FASTER |
Trinotate is a comprehensive annotation suite designed for functional annotation of de novo assembled transcriptomes, particularly for non-model organisms. It provides tools for sequence homology searches, protein domain predictions, functional annotation, and visualization of annotation results. | Bioinformatics, Computational Biology, Transcriptomics, Functional Annotation | Bioinformatics, Biological Sciences | Functional Annotation Tool | Documentation, Uses, and more |
| triton | ACES | Documentation, Uses, and more | ||||
| trnascan-se | Bridges-2 FASTER |
tRNAscan-SE is a program for the identification of transfer RNA (tRNA) genes in genomic sequence. It combines search techniques for computational RNA gene detection and a homology search for analyzing secondary structure features of candidate genes. tRNAscan-SE is widely used for the prediction of tRNA genes in both prokaryotic and eukaryotic genomes. | Bioinformatics, Genomics, Computational Biology, Sequence Analysis | Genomics, Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| tuning analysis utilities | Stampede3 | Documentation, Uses, and more | ||||
| twisted | ACES FASTER |
Twisted is an event-driven networking engine written in Python. It supports multiple network protocols, including TCP, UDP, SSL/TLS, HTTP, IMAP, SSH, and more. Twisted is designed for scalability and to easily build networked applications. | Networking, Event-Driven, Python | Computer & Information Sciences | Library | Documentation, Uses, and more |
| twl-ninja | FASTER | Documentation, Uses, and more | ||||
| txg | FASTER | Documentation, Uses, and more | ||||
| typing-extensions | ACES FASTER |
The typing-extensions module in Python provides additional type hinting support for Python 3.7 and later. It includes type hinting classes that were proposed for inclusion in the main 'typing' module but are specifically intended for external use. | Python, Type Hinting, Typing Module, Type Annotations | Computer & Information Sciences | Python Library | Documentation, Uses, and more |
| ucc | ACES FASTER Stampede3 |
UCC (Universal Chemistry Converter) is a versatile software tool designed to convert chemical structures from one format to another. It supports a wide range of chemical structure file formats, making it an essential utility for chemists and researchers working with molecular structures. | Chemical Software, Chemical Structure Converter, Chemistry | Chemical Sciences, Natural Sciences | Conversion Tool | Documentation, Uses, and more |
| ucc-cuda | ACES FASTER |
ucc-cuda is an open-source compiler that integrates Unified Code Coverage Analysis (UCC) with the CUDA programming model used for parallel computing on NVIDIA GPUs. It allows developers to perform code coverage analysis on CUDA programs to identify unexecuted code paths and improve code quality. | Compiler, Cuda, Code Coverage Analysis, Parallel Computing | Computer & Information Sciences, Engineering & Technology | Development Tool | Documentation, Uses, and more |
| ucsctest | FASTER | UC Solvent Cluster Test (UCSCTest) is a suite of tools for testing parallel quantum chemistry software that uses solvent cluster models. It allows users to easily set up and run tests to evaluate the performance of various quantum chemistry software in the presence of solvent effects. | Quantum Chemistry, Solvent Effects, Performance Evaluation, Benchmarking | Chemical Sciences, Other Chemical Sciences | Tool | Documentation, Uses, and more |
| ucsctools | FASTER | UCSC Genome Browser Utilities, a set of tools that interact with the UCSC Genome Browser database. These tools facilitate various genomic data manipulation tasks. | Genomics, Genome Browser, Data Manipulation, Bioinformatics | Biological Sciences | Library | Documentation, Uses, and more |
| ucx | ACES Anvil Bridges-2 Expanse FASTER KyRIC Ookami Stampede3 |
Unified Communication X (UCX) is a flexible and high-performance communication library for applications and libraries. | Communication Library, High-Performance Computing, Distributed Computing | Engineering & Technology | Communication Library | Documentation, Uses, and more |
| ucx-cuda | ACES FASTER |
ucx-cuda is a CUDA-enabled version of the Unified Communication X (UCX) framework, designed to provide high-performance communication primitives for parallel programming models on NVIDIA GPUs. | Ucx, Cuda, Gpu-Accelerated Computing, Communication Primitives | Computer & Information Sciences | Communication Framework | Documentation, Uses, and more |
| udunits | ACES Anvil FASTER Stampede3 |
UDUNITS supports conversion of unit specifications between formatted, human-readable strings and machine-friendly structures. In addition, UDUNITS defines functions that can be used to identify whether pairs of units are conformable for mathematical operations, to convert numerical values from one unit to another, and to generate strings representing the units of quantities. | Units, Unit Conversion, Udunits | Other Natural Sciences | Conversion Tool | Documentation, Uses, and more |
| umap-learn | ACES FASTER |
Documentation, Uses, and more | ||||
| umi-tools | FASTER | Documentation, Uses, and more | ||||
| uni-core | ACES | Documentation, Uses, and more | ||||
| unicycler | ACES | Unicycler is a hybrid assembly pipeline for bacterial genomes. It can assemble both short and long reads using a combination of de novo assembly and polishing steps. | Bioinformatics, Genomics, Assembly, Bacteria | Genetics, Biological Sciences | Sequence Assembly | Documentation, Uses, and more |
| unidecode | FASTER | Documentation, Uses, and more | ||||
| unifdef | FASTER | Documentation, Uses, and more | ||||
| unifrac | ACES | Documentation, Uses, and more | ||||
| unimap | FASTER | Documentation, Uses, and more | ||||
| unison | FASTER | Unison is a file synchronization and file sharing tool that allows users to synchronize files across multiple devices or directories. It is designed to be efficient, reliable, and easy to use, with support for both one-way and two-way synchronization. | File Synchronization, File Sharing, Cross-Platform Tool | Utility | Documentation, Uses, and more | |
| unzip | ACES FASTER |
Unzip is a popular open-source file extraction utility for extracting compressed files in various formats. It is commonly used to extract files from ZIP archives, but it also supports other archive formats. | File Extraction, Compression, Utility | Computer & Information Sciences | File Extraction | Documentation, Uses, and more |
| upcxx | FASTER | Documentation, Uses, and more | ||||
| uproot | FASTER | Documentation, Uses, and more | ||||
| usearch | FASTER | Documentation, Uses, and more | ||||
| utf8proc | ACES FASTER |
utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. It is written with performance and robustness in mind. | Unicode, Utf-8, Normalization, Case Folding, Character Manipulation | Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| uthash | FASTER | Documentation, Uses, and more | ||||
| util-linux | ACES FASTER KyRIC Ookami |
Util-linux is a suite of essential utilities for any Linux system. It contains various programs for handling basic system functionalities, such as mounting drives, managing partitions, controlling system processes, monitoring system performance, and more. | Linux, System Utilities, Command Line Tools | Computer & Information Sciences | Operating System Tools | Documentation, Uses, and more |
| util-linux-uuid | Anvil DeltaAI KyRIC |
util-linux-uuid is a command-line utility that allows users to generate universally unique identifiers (UUIDs) in various formats. UUIDs are 128-bit numbers used as identifiers for entities in computer systems with a high probability of being unique. | Uuid Generator, Command-Line Utility, Unique Identifier, Data Management | Computer Science, Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| util-macros | DeltaAI KyRIC |
util-macros is a collection of utility macros for C programmers to aid in simplifying common tasks and improving code readability. These macros are designed to enhance the efficiency and maintainability of C code by providing useful functions and utilities. | Programming, Development, C Programming, Utility Macros | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| valgrind | ACES Anvil FASTER Ookami |
Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. It can also be used for cache and thread error detection. | Debugging, Profiling, Development Tool | Computer & Information Sciences | Programming Tool | Documentation, Uses, and more |
| valgrind memory debugger | KyRIC | Documentation, Uses, and more | ||||
| valgrind4hpc | Delta DeltaAI |
Valgrind4HPC is a performance analysis tool suite specifically designed for high-performance computing (HPC) environments. It provides a comprehensive set of tools for profiling, memory debugging, and thread analysis to help optimize and improve the performance of parallel and distributed applications on HPC systems. | Performance Analysis, Hpc Environments, Profiling, Memory Debugging, Thread Analysis, Parallel Programming | Computer & Information Sciences, Engineering & Technology | Tool | Documentation, Uses, and more |
| vasp | ACES Anvil Bridges-2 FASTER Stampede3 |
VASP (Vienna Ab-initio Simulation Package) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. | Materials Modelling, Electronic Structure Calculations, Quantum-Mechanical Simulations, Dft Calculations, Molecular Dynamics | Chemistry, Physical Sciences, Engineering & Technology | Package | Documentation, Uses, and more |
| vawk | FASTER | vawk is a vectorized AWK-like language and runtime designed for efficient and high-performance processing of structured text data. | Text Processing, Data Manipulation, Vectorized Operations | Computer & Information Sciences | Language/Runtime | Documentation, Uses, and more |
| vcf2maf | Bridges-2 | vcf2maf is a tool that annotates variants in VCF files with Variant Effect Predictor (VEP) and converts them to Mutation Annotation Format (MAF). It helps in interpreting and analyzing genetic variants in the context of known genomic annotations. | Bioinformatics, Variant Annotation, Genetic Variants, Annotation Tool | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| vcflib | ACES FASTER |
Documentation, Uses, and more | ||||
| vcftools | ACES Anvil Bridges-2 Delta FASTER |
VCFtools is a software package for manipulating and analyzing genetic variation data stored in Variant Call Format (VCF) files. It provides a wide range of tools for quality control, filtering, summarization, and other analyses of genetic variants. | Genetic Variation Analysis, Variant Call Format (Vcf), Population Genetics, Bioinformatics | Biological Sciences | Data Analysis Tool | Documentation, Uses, and more |
| velvet | ACES | Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as those produced by the Illumina platform. It is efficient in handling large volumes of data and is widely used for assembling genomes, transcriptomes, and metagenomes. | Genomics, Bioinformatics, Sequencing, Assembly | Biological Sciences | Bioinformatics Tool | Documentation, Uses, and more |
| vep | FASTER | The Variant Effect Predictor (VEP) determines the functional consequences of genetic variants. It annotates and predicts the effects of variants such as amino acid changes, regulatory region disruptions, and protein-truncating variants on genes, transcripts, and protein sequences. | Genomics, Bioinformatics, Variant Annotation, Functional Genomics, Variant Analysis | Biological Sciences | Command Line Tool | Documentation, Uses, and more |
| vesta | ACES FASTER |
VESTA is a 3D visualization software for structural models, volumetric data, and crystal structures. It allows users to manipulate and analyze complex molecular and crystal structures with a range of visualization options. | 3D Visualization, Crystallography, Molecular Modeling, Structural Analysis | Chemical Sciences | Scientific Software | Documentation, Uses, and more |
| vg | FASTER | Variation graphs (vg) provides tools for working with genome variation graphs. | Documentation, Uses, and more | |||
| vibrant | FASTER | Documentation, Uses, and more | ||||
| viralrecall | FASTER | Documentation, Uses, and more | ||||
| virsorter2 | FASTER | Documentation, Uses, and more | ||||
| virtualenv | ACES FASTER |
virtualenv is a tool used to create isolated Python environments. These environments can have their own installation directories and can be configured with different versions of Python and packages without affecting the global Python installation on the system. | Python, Virtual Environment, Package Management | Informatics, Analytics & Information Science, Computer & Information Sciences | Environment/Setup Tool | Documentation, Uses, and more |
| virtualgl | ACES FASTER |
VirtualGL is an open-source toolkit that enables the 3D acceleration of applications that are running on a remote server. It redirects the 3D rendering commands from a Unix/Linux OpenGL application onto a server-side GPU and converts the rendered 3D images into a video stream that is sent to the client-side for display using a high-speed network connection. | Remote Rendering, Gpu Acceleration, Opengl Applications, Network Streaming | Computer & Information Sciences | Graphics Software | Documentation, Uses, and more |
| visidata | Bridges-2 | VisiData is a fast, interactive multitool for tabular data. It combines the clarity of a spreadsheet, the efficiency of the terminal, and the power of Python, into a lightweight utility which can handle millions of rows with ease. | Data Manipulation, Visualization, Python, Data Analysis | Computer & Information Sciences | Utility Software | Documentation, Uses, and more |
| visit | Anvil Bridges-2 Delta FASTER Ookami Stampede3 |
Visit is an open-source interactive parallel visualization and graphical analysis tool. It is designed to handle very large data set visualization and enable users to visualize and analyze data from a variety of sources. | Visualization, Data Analysis, Scientific Computing | Informatics, Analytics & Information Science, Computer & Information Sciences | Visualization Software | Documentation, Uses, and more |
| vispy | FASTER | Documentation, Uses, and more | ||||
| visual studio code | Anvil | Documentation, Uses, and more | ||||
| vlc player | Anvil | Documentation, Uses, and more | ||||
| vmd | ACES Anvil Bridges-2 Expanse FASTER Ookami |
Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | Molecular Visualization, Molecular Dynamics, Structural Biology | Biophysics, Biochemistry & Molecular Biology, Biological Sciences | Molecular Visualization Tool | Documentation, Uses, and more |
| vmd cli | Delta | Documentation, Uses, and more | ||||
| vmtouch | DeltaAI | Documentation, Uses, and more | ||||
| voro++ | ACES FASTER Ookami |
Voro++ is an open-source software library for the computation of the Voronoi diagram, a partitioning of space into a set of polygons based on the distance to a specified set of points. It provides a variety of algorithms for constructing Voronoi diagrams in both two and three dimensions. | Voronoi Diagram, Computational Geometry, Open-Source | Mathematics | Library | Documentation, Uses, and more |
| vpl | KyRIC | VPL (Visual Programming Language) is a software tool that allows users to create programs by manipulating graphical elements rather than by specifying them textually. It provides a visual interface for programming tasks, making it easier for beginners to understand programming concepts and create functioning code. | Visual Programming, Beginner-Friendly, Graphical Interface | Computer & Information Sciences | Language Programming | Documentation, Uses, and more |
| vscode | ACES FASTER |
A popular, extensible text editor from Microsoft | Documentation, Uses, and more | |||
| vsearch | ACES FASTER |
VSEARCH is a versatile open-source tool for metagenomics and sequence analysis. It supports DNA and RNA sequence analysis, clustering, dereplication, chimera detection, pairwise alignment, searching, and filtering. | Metagenomics, Sequence Analysis, Bioinformatics | Bioinformatics, Biological Sciences | Sequence Analysis Tool | Documentation, Uses, and more |
| vt | FASTER | Documentation, Uses, and more | ||||
| vtk | ACES Anvil Delta FASTER |
The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world. VTK offers a wide range of functionality for tasks such as scientific visualization, medical imaging, computational fluid dynamics, and more. | 3D Computer Graphics, Image Processing, Scientific Visualization, Medical Imaging, Computational Fluid Dynamics | Physical Sciences | Visualization | Documentation, Uses, and more |
| vtune | ACES FASTER KyRIC Stampede3 |
VTune Profiler is a performance profiling tool for optimizing application performance on Intel architecture. It provides deep insights to help you understand and improve performance and power characteristics of your application. | Performance Optimization, Profiling, Intel Architecture | Computer & Information Sciences | Profiling Tool | Documentation, Uses, and more |
| vulkansdk | ACES FASTER |
The Khronos Vulkan API is an explicit, low-overhead, cross-platform graphics and compute API. | Documentation, Uses, and more | |||
| wandb | ACES FASTER |
Documentation, Uses, and more | ||||
| wannier90 | Anvil FASTER |
Wannier90 is a tool used for the computation of maximally-localized Wannier functions, which are spatially compact and localized functions that provide a natural description of the electronic structure of a solid. These functions are often used in condensed matter physics calculations to study the electronic properties of materials. | Computational Chemistry, Solid State Physics, Electronic Structure, Materials Science | Condensed Matter Physics, Physical Sciences | Library | Documentation, Uses, and more |
| wayland | ACES FASTER |
Wayland is a communication protocol that specifies the communication between a display server and its clients, as well as a reference implementation of the protocol in the C programming language. | Display Server, Communication Protocol, Graphics Rendering | Computer & Information Sciences | Communication Protocol Implementation | Documentation, Uses, and more |
| waylandpp | ACES FASTER |
waylandpp is a C++ binding library for Wayland, which is a protocol for a compositor to talk to its clients. | Wayland, C++, Binding Library | Computer & Information Sciences | Programming Interface | Documentation, Uses, and more |
| webkitgtk+ | ACES FASTER |
WebKitGTK+ is an open-source web browser engine. It is a GTK+ port of the WebKit engine. It offers a framework for rendering web content in applications built with GTK+. | Web Browser Engine, Gtk+ Port, Open-Source, Web Content Rendering | Computer & Information Sciences | Rendering Engine | Documentation, Uses, and more |
| webproxy | ACES FASTER |
WebProxy is a tool that allows users to access websites anonymously by hiding their IP address. It acts as an intermediary between the user's device and the internet, masking the user's IP address and encrypting their internet traffic for increased privacy and security. | Proxy Server, Internet Privacy, Security, Anonymity | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| westpa | Delta | The Weighted Ensemble Simulation Toolkit for the Analysis of Rare Events (WESTPA) is an open-source software package designed to facilitate the description and analysis of rare events in complex systems. It employs a weighted ensemble-based strategy to efficiently sample and explore the configuration space of a system, particularly when traditional molecular dynamics simulations may struggle to capture rare events. | Molecular Dynamics, Simulation Analysis, Rare Events, Complex Systems, Open-Source | Biophysics, Biological Sciences | Computational Software | Documentation, Uses, and more |
| wfa2 | ACES FASTER |
Documentation, Uses, and more | ||||
| wfmash | FASTER | Documentation, Uses, and more | ||||
| wget | ACES FASTER |
GNU Wget is a utility for non-interactive download of files from the Web. It supports HTTP, HTTPS, and FTP protocols, as well as retrieval through HTTP proxies. | Download Manager, Command-Line Tool | Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| wgsim | FASTER | Documentation, Uses, and more | ||||
| whatshap | FASTER | Whatshap is a software tool for phasing genomic variants, which refers to the process of determining the parental origin of alleles in an individual's genome. It focuses on handling variants such as single nucleotide polymorphisms (SNPs) and indels. | Genomics, Bioinformatics, Variant Phasing | Biological Sciences | Tool | Documentation, Uses, and more |
| which | DeltaAI | Documentation, Uses, and more | ||||
| wiggletools | FASTER | WiggleTools is a software library for the analysis and visualization of data stored in the common genomics Wiggle track format (WIG), allowing researchers to efficiently manipulate, aggregate, and visualize large-scale genomic datasets. | Genomics, Bioinformatics, Data Analysis, Visualization | Bioinformatics, Biological Sciences | Data Analysis | Documentation, Uses, and more |
| winnowmap | FASTER | WinnowMap is a software tool for mapping and alignment of long nanopore and PacBio sequencing reads to large reference genomes. | Mapping, Alignment, Nanopore, Pacbio, Sequencing | Genetics, Biological Sciences | Sequence Alignment Tool | Documentation, Uses, and more |
| wolfpsort | FASTER | Documentation, Uses, and more | ||||
| wpebackend-fdo | ACES FASTER |
wpebackend-fdo is a software project that provides a backend implementation for WebKit's WPE WebKit using a Flatpak distributed runtime for sandboxing. | Software, Sandboxing, Integration, Performance Optimization | Computer Science, Computer & Information Sciences | Backend Implementation | Documentation, Uses, and more |
| wps | ACES FASTER |
WPS Office is a comprehensive office suite that includes Writer, Presentation, and Spreadsheets. It provides a familiar interface and full compatibility with Microsoft Office file formats. | Office Suite, Word Processing, Presentation, Spreadsheets, Pdf Editing | Other | Office Suite | Documentation, Uses, and more |
| wrapt | FASTER | Documentation, Uses, and more | ||||
| wrf | ACES FASTER |
The Weather Research and Forecasting (WRF) model is a next-generation mesoscale numerical weather prediction system designed to serve both atmospheric research and operational forecasting needs. It features multiple options for parameterizations, data assimilation techniques, and model domains, allowing for simulations at various spatial and temporal scales. | Weather Forecasting, Numerical Modeling, Atmospheric Science | Earth & Environmental Sciences | Meteorological Modeling Software | Documentation, Uses, and more |
| wtdbg2 | FASTER | Documentation, Uses, and more | ||||
| wxpython | ACES FASTER |
wxPython is a cross-platform GUI toolkit for the Python programming language. It allows Python programmers to create functional and native-looking user interfaces for their applications. | Gui Toolkit, Cross-Platform, Python | Computer & Information Sciences | Library | Documentation, Uses, and more |
| wxwidgets | ACES FASTER |
wxWidgets is a C++ library that lets developers create applications for Windows, macOS, Linux and other platforms with a single code base. It is a mature and comprehensive framework that allows for native user interfaces with a wide range of widgets. | Gui Library, Cross-Platform Development, Native User Interfaces, Open-Source Software | Engineering & Technology | Library/Framework | Documentation, Uses, and more |
| x11 | ACES FASTER |
X11 is a windowing system for bitmap displays, common on Unix-like operating systems and desktop environments. It provides the basic framework for building GUI applications on these systems, handling graphical elements such as windows, menus, and user input. | Windowing System, Gui Applications, Unix-Like Operating Systems | Computer & Information Sciences | System Software | Documentation, Uses, and more |
| x264 | ACES FASTER |
x264 is a free and open-source software library and a command-line utility for encoding video streams into the H.264/MPEG-4 AVC format. | Video Encoding, H.264/Mpeg-4 Avc, Open-Source | Engineering & Technology | Video Encoding | Documentation, Uses, and more |
| x265 | ACES FASTER |
x265 is a free and open-source software library and application for encoding video streams into the H.265/MPEG-H HEVC (High Efficiency Video Coding) format. It is widely used for efficient video compression and playback on various platforms. | Video Encoding, Compression, Hevc | Computer & Information Sciences | Library & Application | Documentation, Uses, and more |
| xalt | Anvil Jetstream2 Stampede3 |
XALT (XALT Accounting for Loadable and Transient Objects) is a tool designed to track the detailed usage of HPC systems by monitoring library dependencies and executables during job executions. It captures information on modules, compilers, libraries, and executables used in each job, providing detailed insights into the software stack and usage patterns on the HPC system. | Hpc, Monitoring | Engineering & Technology | Performance Tracking | Documentation, Uses, and more |
| xarray | ACES FASTER |
Xarray is an open source Python library that provides data structures and functions for working with labelled multidimensional arrays. It aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. | Python Library, Data Analysis, Scientific Computing, Multidimensional Arrays | Other Natural Sciences | Library | Documentation, Uses, and more |
| xcb-proto | Anvil DeltaAI FASTER |
Documentation, Uses, and more | ||||
| xcb-util-image | Anvil | The xcb-util-image library provides a number of functions used for manipulating and creating XCB format images, including loading and saving images to disk in various formats. | Image Processing, Xcb, Library | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xcb-util-keysyms | Anvil | The xcb-util-keysyms library provides utility functions for obtaining the keysyms keycode values, as used in the X Window System, as well as common XKB functions. It is part of the X C Bindings (XCB) utility libraries which provide a number of convenience functions and interfaces for usage with XCB. | X Window System, Utility Functions, Xcb | Computer Science, Computer & Information Sciences | Utility | Documentation, Uses, and more |
| xcb-util-renderutil | Anvil | A set of libraries which provide a convenient API for rendering text with XCB. | Xcb, Rendering, Text, Api | Computer & Information Sciences | Rendering | Documentation, Uses, and more |
| xcb-util-wm | Anvil | xcb-util-wm is a set of utility functions for interfacing with the X Window Manager (WM) extension of the XCB library. It provides a number of functions that are useful to XCB WM clients. | X Window System, Window Manager, Xcb Library, Utility Functions | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| xclock | Delta | xclock is a simple graphical user interface (GUI) application that displays a digital or analog clock on the user's desktop. It is commonly found on Unix and Unix-like operating systems, serving as a basic utility for users to check the current time visually. | Clock Utility, Gui Application | Other Computer & Information Sciences | Desktop Application | Documentation, Uses, and more |
| xcrysden | FASTER | Documentation, Uses, and more | ||||
| xdinfo | Bridges-2 Expanse |
xdinfo is a Python package which provides information about X-ray diffraction (XD) like functions, atomic scattering, Mueller matrix, XD profiles, and more. It is designed for the analysis and interpretation of X-ray diffraction data in various scientific applications. | Python Package, X-Ray Diffraction Analysis, Scientific Data Interpretation | Physical Sciences | Library | Documentation, Uses, and more |
| xdresourceid | Bridges-2 | xdResourceID is a tool used for identifying and managing unique resource identifiers within a digital environment. It provides a systematic approach to assigning and tracking identifiers for various digital resources. | Resource Management, Digital Environment, Identifier Tracking | Engineering & Technology | Documentation, Uses, and more | |
| xdusage | Bridges-2 | xdusage is a tool used for monitoring and analyzing batch job resource utilization on High Performance Computing (HPC) systems. It allows users to track resource usage, such as CPU time, memory, and disk space, for individual jobs or users. | Hpc, Resource Monitoring, Batch Job Management, Performance Analysis | Infrastructure & Instrumentation, Engineering & Technology | Command Line Tool | Documentation, Uses, and more |
| xengsort | FASTER | Documentation, Uses, and more | ||||
| xerces-c | Delta | Xerces-C is a validating XML parser written in C++. | Xml Parser, Validation, C++, Unicode | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xerces-c++ | ACES FASTER |
Xerces-C++ is a validating XML parser written in C++ and released by the Apache Software Foundation. It is a high-performance, feature-rich parser that is widely used for parsing and processing XML documents in a variety of applications. | Xml Parser, Data Processing, Software Development | Computer & Information Sciences | Parser | Documentation, Uses, and more |
| xextproto | Anvil Delta DeltaAI FASTER |
X11 Extension protocols and auxiliary headers | Linux, X11, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xeyes | Delta | Documentation, Uses, and more | ||||
| xfce4 | FASTER | Documentation, Uses, and more | ||||
| xfconf | FASTER | Documentation, Uses, and more | ||||
| xfdesktop | FASTER | Documentation, Uses, and more | ||||
| xfwm4 | FASTER | Documentation, Uses, and more | ||||
| xgboost | ACES FASTER |
XGBoost is an open-source software library which provides a gradient boosting framework for efficient and high-performance machine learning. | Machine Learning, Gradient Boosting, Ensemble Learning | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems | Library | Documentation, Uses, and more |
| xlsxwriter | ACES FASTER |
Documentation, Uses, and more | ||||
| xml-compile | FASTER | Documentation, Uses, and more | ||||
| xml-libxml | ACES FASTER |
xml-libxml is a software library for reading, writing, and manipulating XML files. It provides a robust set of tools for parsing and processing XML documents. | Xml, Parser, Library, Data Processing | Other Computer & Information Sciences, Computer & Information Sciences | Data Processing | Documentation, Uses, and more |
| xmltodict | ACES FASTER |
Documentation, Uses, and more | ||||
| xorg-macros | ACES FASTER |
The xorg-macros package provides a set of autoconf macros used by X.org software packages for consistent and simplified build procedures across various Unix and Linux systems. | Build Tools, Autoconf Macros | Computer & Information Sciences | Library/Dependency | Documentation, Uses, and more |
| xpmem | ACES DeltaAI FASTER Ookami |
XPMEM is a kernel module that provides a kernel-level interface for sharing memory between processes. | Kernel Module, Inter-Process Communication, Memory Sharing | Computer Science, Computer & Information Sciences | System Software | Documentation, Uses, and more |
| xprop | ACES FASTER |
xprop is a utility for retrieving the properties of a window in a X server system. It allows users to query and display properties of a given X server window, which can be useful for debugging and troubleshooting GUI-related issues. | X Server, Window Properties, Gui Debugging | Computer Science, Computer & Information Sciences | System Tool | Documentation, Uses, and more |
| xproto | ACES Anvil Delta DeltaAI FASTER |
X Window System protocol development files. | Software Development, Protocol Development, X Window System | Computer & Information Sciences | Library | Documentation, Uses, and more |
| xtalopt | FASTER | xtalopt is a genetic algorithm-based crystal structure prediction software that aims to predict the structure of a material given its composition. It helps in exploring the possible crystallographic structures and configurations of materials. | Crystal Structure Prediction, Material Science, Genetic Algorithm, Computational Chemistry | Materials Science, Physical Sciences | Prediction Software | Documentation, Uses, and more |
| xtb | FASTER | Documentation, Uses, and more | ||||
| xtensor | FASTER | Documentation, Uses, and more | ||||
| xterm | DeltaAI | Documentation, Uses, and more | ||||
| xtrans | Delta DeltaAI FASTER |
xtrans is a general-purpose transducer-based approach for defining translations between various formats and data representations. It provides a flexible framework for specifying bidirectional transformations between different data structures. | Data Transformation, Format Conversion, Transducer-Based Tool | Computer & Information Sciences | Tool | Documentation, Uses, and more |
| xvfb | ACES FASTER |
Xvfb (X virtual framebuffer) is an in-memory display server for Unix-like systems that enable running graphical applications without a display. | Display Server, Headless, Virtual Display | Computer & Information Sciences | Virtual Display Server | Documentation, Uses, and more |
| xxd | ACES FASTER |
xxd is a command-line utility on Unix and Unix-like systems for creating a hex dump of a given file or standard input. | Hex Dump, Command-Line Utility, Data Conversion | Other Computer & Information Sciences | Command-Line Tool | Documentation, Uses, and more |
| xz | ACES Anvil Delta DeltaAI FASTER KyRIC |
xz is a free and open-source data compression tool that uses the LZMA compression algorithm. It is designed to be an efficient and high-performance compression utility. | Compression, Data Compression, Open-Source | Computer & Information Sciences | Utility | Documentation, Uses, and more |
| yacs | ACES FASTER |
YACS (Yet Another Constraint Solver) is a Python-based constraint satisfaction problem (CSP) solver that allows for the modeling and solving of constraint problems using a high-level interface. | Constraint Satisfaction Problem, Csp Solver, Python-Based, Constraint Modeling | Computer & Information Sciences | Optimization Tool | Documentation, Uses, and more |
| yaff | FASTER | The Yet Another Force Field (YAFF) tool is a versatile Python library for developing force fields and running molecular dynamics simulations. It provides efficient implementations of force fields along with tools for parameterizing various interactions. | Molecular Dynamics, Force Field Development, Python Library | Biophysics, Natural Sciences | Python Library | Documentation, Uses, and more |
| yahs | FASTER | Documentation, Uses, and more | ||||
| yak | FASTER | Documentation, Uses, and more | ||||
| yaml | Ookami | YAML (YAML Ain't Markup Language) is a human-readable data serialization format that is commonly used for configuration files, data exchange, and structured data representation. It aims to be easily readable by humans and supports various data structures and nested data hierarchies, making it a popular choice for configuration management and data storage. | Information Technology | Serialization Language | Documentation, Uses, and more | |
| yasm | ACES Delta FASTER |
Yasm is a complete rewrite of the NASM assembler under the new BSD License. It is designed to have NASM compatibility for NASM's source code usage. Yasm currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, COFF, Mach-O (32 and 64), RDOFF2, SREC, and Hex formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats. | Assembler, Assembly, Development, Programming | Engineering & Technology | Assembler | Documentation, Uses, and more |
| yaxt | ACES FASTER |
YAXT (Yet Another XTabulator) is a Python library for creating publication-ready quantitative tables with an emphasis on simplicity and customization. It provides a straightforward interface for generating tables directly from pandas DataFrames. | Python Library, Data Analysis, Table Generation | Computer & Information Sciences | Library | Documentation, Uses, and more |
| yell | ACES | Documentation, Uses, and more | ||||
| z3 | ACES FASTER |
Z3 is a high-performance theorem prover being developed at Microsoft Research. Z3 is a state-of-the-art SMT (Satisfiability Modulo Theories) solver used in various applications including software and hardware verification, security, AI and ML, and more. It provides a programming interface for both C and Python. | Theorem Prover, Satisfiability Modulo Theories (Smt) Solver, Software Verification, Hardware Verification, Security, Ai, Machine Learning | Computer & Information Sciences | Theorem Prover | Documentation, Uses, and more |
| zarr | ACES FASTER |
Zarr is a Python package providing an implementation of chunked, compressed, N-dimensional arrays which can be stored in memory, on disk, or on cloud storage. It is designed to efficiently store and retrieve large arrays of data while minimizing the use of computational resources. | Python Library, Data Storage, Data Management | Computer & Information Sciences | Library | Documentation, Uses, and more |
| zebulon | FASTER | Zebulon is a computational software designed for protein structure prediction using deep learning methods. | Computational Software, Protein Structure Prediction, Deep Learning, Bioinformatics | Bioinformatics, Biological Sciences | Computational | Documentation, Uses, and more |
| zeromq | ACES FASTER |
ZeroMQ is a high-performance asynchronous messaging library that is designed for building distributed and concurrent applications. It provides messaging patterns like pub-sub, request-reply, push-pull, etc., along with sockets and transports for communication between nodes. | Messaging, Distributed Computing, Async | Computer & Information Sciences | Communication | Documentation, Uses, and more |
| zfp | ACES FASTER |
zfp is a compressed numerical array library providing high-throughput, low-overhead fixed-rate, fixed-precision encoding and compression of 1D and 2D scientific data. | Numerical Array, Compression, Scientific Data | Computer & Information Sciences | Library | Documentation, Uses, and more |
| zip | ACES FASTER |
zip is a compression and file packaging utility for Unix, VMS, DOS, OS/2, Windows 9x/NT/XP, Minix, Atari, Macintosh, Amiga, and Acorn RISC OS. | Compression, File Packaging, Utility | Other Computer & Information Sciences | Utility | Documentation, Uses, and more |
| zlib | ACES Anvil DeltaAI FASTER KyRIC Stampede3 |
zlib is a software library for data compression that provides functions for file compression and decompression using the DEFLATE compression algorithm. It is widely used in various applications for reducing file size and conserving storage space. | Compression, Data Compression, File Compression, Deflate Algorithm | Computer & Information Sciences | Data Compression | Documentation, Uses, and more |
| zlib-ng | Delta DeltaAI |
Documentation, Uses, and more | ||||
| zoltan | ACES Bridges-2 |
Zoltan is a toolkit for managing parallel memory for dynamic applications in high-performance computing environments. It provides scalable parallel dynamic load-balancing, graph partitioning, and dynamic data restructuring services. | Parallel Computing, High-Performance Computing, Dynamic Applications | Engineering & Technology | Hpc Tools | Documentation, Uses, and more |
| zsh | Ookami | Zsh is a powerful and customizable UNIX shell with a large set of features aimed at improving user experience and productivity. It is an extended Bourne shell with many improvements, including interactive command line editing, programmable command completion, advanced scripting capabilities, and theme support. | Unix Shell, Customizable Shell, Command Line Interface | Computer & Information Sciences | Command Line Interface | Documentation, Uses, and more |
| zstd | ACES DeltaAI Expanse FASTER KyRIC |
Zstandard (or zstd) is a fast data compression algorithm developed by Facebook. It is designed to provide high compression ratios with very low latency, making it suitable for real-time compression/decompression scenarios. Zstandard offers a wide range of compression levels, from very fast to very strong, allowing users to balance between speed and compression ratio based on their requirements. | Compression, Data Compression, Algorithm | Computer Science, Computer & Information Sciences | Compression Algorithm | Documentation, Uses, and more |