Software Documentation
The following software is reported as available on ACES by the Software Documentation Service.
Available Software
| Application | Description | Research Discipline |
|---|---|---|
| abaqus | 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. | Mechanical Engineering |
| abseil | 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. | Computer & Information Sciences |
| absl-py | absl-py is a Python library developed by Google that provides common utilities for building and running applications, including command-line flag parsing, logging, and application initialization. It helps standardize Python program structure and is widely used in large-scale and machine learning projects. | Software Engineering |
| abyss | 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. | Biological Sciences |
| accelerate | Accelerate is a lightweight library that simplifies running PyTorch training and inference across different hardware setups, including CPUs, GPUs, TPUs, and distributed environments. It abstracts away the complexity of distributed and mixed-precision training, allowing the same codebase to scale from local development to large multi-node deployments. | |
| actc | 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. | Computer & Information Sciences |
| adaptivecpp | ||
| adios2 | 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. | Computer & Information Sciences |
| ai-tools-gpu | A collection of software tools at all levels of the AI stack unlock the full capabilities of Intel hardware. All Intel AI tools and frameworks are built on the foundation of a standards-based, unified oneAPI programming model that helps get the most performance from end-to-end pipelines on all available hardware. Description Source: https://www.intel.com/content/www/us/en/developer/topic-technology/artificial-intelligence/frameworks-tools.html | |
| aiohttp | 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. | Computer & Information Sciences |
| aishell | AI Shell is an interactive shell that provides a chat interface with language models. The shell provides agents that connect to different AI models and other assistance providers. Users can interact with the agents in a conversational manner. Description Source: https://learn.microsoft.com/en-us/powershell/utility-modules/aishell/overview | |
| alphafast | AlphaFast is a high-throughput protein structure prediction pipeline that accelerates AlphaFold3 inference using GPU-accelerated MMSeqs2 for fast sequence searching. It enables ultra-fast generation of protein structural models by optimizing the AlphaFold workflow for large-scale applications. | Biochemistry and Molecular Biology |
| alphafold | AlphaFold is a deep learning-based system developed by DeepMind to predict protein folding and 3D structure with high accuracy. | Biochemistry and Molecular Biology |
| alphafold3 | AlphaFold 3 is DeepMind’s next-generation AI system for predicting the structure and interactions of biological molecules, extending beyond proteins to model complexes involving DNA, RNA, ligands, ions, and other biomolecules. It enables high-accuracy structural predictions that support drug discovery, molecular biology, and biomedical research. | Biochemistry and Molecular Biology |
| alphapickle | Alphapickle is a Python library that provides tools and utilities for working with alpha factors and optimizing portfolio construction in quantitative finance. | Other Mathematics |
| alphapulldown | AlphaPulldown is a computational tool built around AlphaFold that enables systematic prediction of protein–protein interactions and complex structures at scale. It automates the generation, execution, and analysis of AlphaFold runs to efficiently screen many protein combinations. | |
| alsa-lib | 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. | Computer & Information Sciences |
| amber | 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. | Biological Sciences |
| ambertools | 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. | Biological Sciences |
| anaconda3 | 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. | Computer & Information Sciences |
| anadama2 | Anadama2 is a workflow management system designed for reproducible scientific computing. It allows users to define, execute, and manage complex workflows in a flexible and user-friendly manner. | Computational Biology |
| anicalculator | ANIcalculator is a bioinformatics tool that computes Average Nucleotide Identity (ANI) and alignment fraction between two genomes, commonly used for microbial genome comparison and species delineation. | Biological Sciences |
| annevo | ||
| annovar | ANNOVAR is a powerful software tool designed to annotate genetic variants detected from diverse genomes. | Biological Sciences |
| ant | 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. | Computer Science |
| antlr | ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files. | Other Computer and Information Sciences |
| aocc | The AMD Optimizing C/C++ Compiler (AOCC) is a high performance compiler suite with support for C, C++, and Fortran programming languages. | Computer & Information Sciences |
| aocl-blas | AOCL BLAS is a high-performance implementation of the Basic Linear Algebra Subprograms (BLAS) for AMD architectures, optimized for performance on AMD processors. | Applied Mathematics |
| apbs | APBS (Adaptive Poisson-Boltzmann Solver) is a software package for solving the Poisson-Boltzmann equation, which is essential for understanding electrostatic interactions in biomolecules. | Biochemistry and Molecular Biology |
| apr | The Apache Portable Runtime (APR) is a software library that provides a predictable and consistent interface to underlying platform-specific implementations. | Engineering & Technology |
| apr-util | 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. | Software Engineering |
| archspec | 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. | Computer & Information Sciences |
| argobots | Argobots is a lightweight and high-performance user-level threading and tasking library designed for high-performance computing applications. It provides a flexible and efficient way to manage concurrency and parallelism in applications. | Computer Science |
| aria2 | aria2 is a lightweight multi-protocol & multi-source command-line download utility. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink. | Computer & Information Sciences, Other Computer & Information Sciences |
| arm-gnu-toolchain | 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. | Engineering & Technology |
| arm-gnu-toolchaint | 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. | Computer Science |
| armadillo | 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. | Computer & Information Sciences |
| arpack-ng | 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. | Physical Sciences |
| arrow | 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. | Computer & Information Sciences |
| arrow-r | 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. | Mathematics |
| ase | Atomistic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing, and analyzing atomistic simulations. | Other Natural Sciences |
| assimp | 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 | Computer & Information Sciences |
| astropy | 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. | Physical Sciences |
| at-spi2-atk | 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. | Computer & Information Sciences |
| at-spi2-core | AT-SPI (Assistive Technology Service Provider Interface) is a protocol that allows assistive technologies to interact with and control applications. | Computer Science |
| atk | 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. | Physical Sciences |
| attr | attr is a command-line utility for managing extended attributes on files in Linux and Unix-like operating systems. It allows users to set, get, list, and remove extended attributes associated with files, which are metadata not interpreted by the filesystem but used by user-space applications. | Computer Science |
| attrdict3 | 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. | Computer & Information Sciences |
| augustus | 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. | Biological Sciences |
| autoconf | 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. | Engineering & Technology |
| autodock-gpu | 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. | Biological Sciences |
| autodock-vina | AutoDock Vina is an open-source program for performing molecular docking, which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. | Molecular Docking |
| automake | Automake is a build automation tool that automatically generates makefiles for software compilation. | Engineering & Technology |
| autotools | 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. | Computer & Information Sciences |
| avogadro2 | Avogadro 2 is an advanced molecular editor and visualization tool designed for computational chemistry and molecular modeling. | Molecular Visualization |
| awscli | 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. | Computer & Information Sciences |
| bamtools | 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. | Biological Sciences |
| bazel | Bazel is a build tool that helps to build and test software of any size, quickly and reliably. | Engineering & Technology |
| bazelisk | Bazelisk is a wrapper for Bazel that automatically downloads and installs the correct version of Bazel for your project. | Software Engineering |
| bbmap | 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. | Biological Sciences |
| bcftools | 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. | Biological Sciences |
| bcrypt | bcrypt is a password hashing function designed by Niels Provos and David Mazières, based on the Blowfish cipher. It is intended to be computationally intensive to resist brute-force attacks. | Cryptography |
| beautifulsoup | Beautiful Soup is a Python library for parsing HTML and XML documents. It creates parse trees from page source codes that can be used to extract data easily. | Informatics |
| bedops | 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. | Biological Sciences |
| bedtools | Bedtools is a software suite for the comparison, manipulation, and annotation of genomic features in multiple formats. | Biological Sciences |
| benchmark | benchmark (Google Benchmark) is an open-source C++ microbenchmarking library that times individual code snippets with high precision. Benchmarks are written as functions registered with the BENCHMARK macro and compiled against the library; the resulting executable runs each one and reports timing statistics. It builds with CMake or Bazel and is widely used to track and compare C++ performance. | Computer Science |
| bindcraft | BindCraft is a user-friendly and accurate computational pipeline designed for de novo protein binder design. It integrates structure-based modeling and design protocols to enable researchers to create novel protein binders with high affinity and specificity. | Biochemistry and Molecular Biology |
| binutils | Binutils is a collection of binary tools, including linker (ld), assembler (as), archiver (ar), and other tools to manipulate object files and executables. | Computer & Information Sciences |
| bio-searchio-hmmer | bio-searchio-hmmer (Bio::SearchIO::hmmer) is a BioPerl module that parses the output of the HMMER sequence-analysis suite. Working through the Bio::SearchIO framework, it reads results from HMMER2 and HMMER3 programs such as hmmsearch, hmmscan, and hmmpfam, and exposes them as structured Perl objects — results, hits, and HSPs — for downstream use in bioinformatics pipelines. | Biological Sciences |
| biom-format | 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 Sciences |
| bioperl | 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. | Biological Sciences |
| biopython | 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 Sciences |
| bison | 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. | Computer & Information Sciences |
| bitsandbytes | BitsAndBytes is a library designed to optimize the memory usage and performance of deep learning models by providing efficient data types and quantization techniques. | Artificial Intelligence and Intelligent Systems |
| blast+ | 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. | Biological Sciences |
| blat | 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. | Biological Sciences |
| blender | 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. | Engineering & Technology |
| blis | 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. | Computer & Information Sciences |
| block | BLOCK is an electronic-structure program implementing the ab initio density matrix renormalization group (DMRG) algorithm for quantum chemistry. It targets strongly correlated, multireference systems with active spaces too large for full configuration interaction, and is commonly used as the active-space solver for CASCI and CASSCF calculations through its interface with the PySCF package. It can run as a standalone command-line program or as a solver within a Python-driven workflow. | Physical Chemistry |
| blosc | Blosc is a high-performance compressor optimized for binary data, designed to speed up the storage and transmission of large datasets. | Applied Computer Science |
| blosc2 | 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. | Computer & Information Sciences |
| bokeh | 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. | Computer & Information Sciences |
| boltz-1 | boltz-1 is a Python-based toolkit designed for predicting and analyzing PROTAC-mediated ternary complexes by integrating AlphaFold3 with advanced modeling techniques. It facilitates structural modeling, fine-tuning, and domain-specific adaptation to enhance the accuracy of protein-ligand interaction predictions in drug discovery. | Biochemistry and Molecular Biology |
| boost | 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. | Computer & Information Sciences |
| boost.mpi | Boost.MPI is a peer-reviewed, free, open-source, portable, and fully-standard library implementation of the Message Passing Interface (MPI) for C++. | Computer & Information Sciences |
| boost.python | 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. | Computer & Information Sciences |
| boto3 | Boto3 is the Amazon Web Services (AWS) SDK for Python, which allows developers to create, configure, and manage AWS services using Python code. | Computer Science |
| bowtie | 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. | Biological Sciences |
| bowtie2 | 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. | Biological Sciences |
| brotli | 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. | Computer Science |
| brotli-python | 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. | Computer & Information Sciences |
| brunsli | 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. | Computer & Information Sciences |
| bsbolt | BSBolt is a bioinformatics software toolkit for efficient alignment, methylation calling, and variant analysis of bisulfite sequencing data. It provides a fast, integrated pipeline for whole-genome and targeted bisulfite sequencing, optimized for accuracy and scalability. | Bioinformatics |
| btllib | btllib is a C++ common code library developed by the Bioinformatics Technology Lab (BirolLab) that provides reusable components and utilities to support bioinformatics software development. | Biological Sciences |
| bucky | This module loads all of the software required for the ETSU Bioinformatics Course | |
| build | 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. | Engineering & Technology |
| busco | 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. | Biological Sciences |
| bwa | 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. | Biological Sciences |
| bwa-mem2 | bwa-mem2 is a fast and accurate alignment tool for mapping DNA sequences against a reference genome, designed to handle large datasets efficiently. | Genomics |
| bwa-meth | BWA-Meth is a software tool for aligning bisulfite-treated sequencing reads to a reference genome, enabling the analysis of DNA methylation. | Biological Sciences |
| bwidget | Bwidget is a collection of useful widgets for the Tcl/Tk GUI toolkit, providing enhanced functionality and improved aesthetics for applications. | Other Computer and Information Sciences |
| bx-python | bx-python is a Python library for bioinformatics that provides tools for manipulating and analyzing biological data, particularly in the context of genomic data. | Genomics |
| bzip2 | 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. | Computer & Information Sciences |
| c-ares | 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. | Computer & Information Sciences |
| cairo | 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. | Computer & Information Sciences |
| camus | CAMUS is an open, fully-annotated 2D echocardiography dataset for cardiac structure segmentation and functional assessment. It comprises apical two- and four-chamber ultrasound sequences from 500 patients, with manual reference contours of the left ventricular endocardium and epicardium and the left atrium at end-diastolic and end-systolic phases, plus image-quality labels and clinical indices such as ejection fraction. It is widely used as a benchmark for training and evaluating deep-learning segmentation methods in echocardiography, and is released for non-commercial research use. | Health Sciences |
| capnproto | Cap'n Proto is an open-source data interchange format that is designed for high performance. It is used for serialization and deserialization of data structures, allowing for efficient data exchange between different systems. | Other Computer and Information Sciences |
| capstone | 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. | Computer & Information Sciences |
| captum | 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. | Computer & Information Sciences |
| cartopy | 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. | Physical Sciences |
| catch | CATCH (Compact Aggregation of Targets for Comprehensive Hybridization) is an open-source Python tool for computational probe design in targeted sequencing. It takes collections of unaligned genomic sequences and computes optimal sets of capture oligonucleotides that fully cover the input diversity while satisfying a user-specified constraint on the number of probes. Developed to enrich diverse viral and microbial genomes in metagenomic samples, it supports pooling multiple species, blacklisting unwanted sequences, customizable hybridization models, and locality-sensitive hashing for scalability. | Biological Sciences |
| catch2 | 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. | Engineering & Technology |
| cbc | CBC (Coin-or branch and cut) is an open-source mixed integer programming solver that is part of the COIN-OR (Computational Infrastructure for Operations Research) project. It is designed to handle large-scale optimization problems efficiently. | Mathematics |
| ccache | 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. | Engineering & Technology |
| cd-hit | 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. | Biological Sciences |
| cdo | Climate Data Operators (CDO) is a collection of command-line operators for manipulating and analyzing climate and numerical weather prediction (NWP) model data. | Earth & Environmental Sciences |
| cdsapi | 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). | Earth & Environmental Sciences |
| cereal | Cereal is a C++11 library for serialization. It is designed to be fast, compact, and have an easy-to-use API. | Computer & Information Sciences |
| ceres-solver | Ceres Solver is an open-source C++ library for modeling and solving large, complicated optimization problems. | Applied Mathematics |
| cesm-deps | 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. | Earth & Environmental Sciences |
| cffi | 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. | Computer & Information Sciences |
| cfitsio | CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. | Physical Sciences |
| cgal | 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. | Computer & Information Sciences |
| cgl | Cgl (COIN-OR Cut Generation Library) is an open-source C++ library implementing a wide range of cutting-plane algorithms that tighten the linear-programming relaxations of mixed-integer programs. It bundles many independent cut generators, including Gomory, lift-and-project, mixed-integer rounding, flow-cover, clique, and probing cuts, behind a common interface, and interoperates with solvers such as Cbc, Clp, and BCP through the Osi abstraction rather than solving models directly. It is released under the Eclipse Public License. | Computer Science |
| cgns | 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. | Physical Sciences |
| chameleon | 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. | Other Computer & Information Sciences |
| check | 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/ | |
| checkm | 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. | Biological Sciences |
| checkm-database | CheckM-database is a curated collection of reference genomes and marker gene sets used by the CheckM software to assess the quality of microbial genomes, including completeness and contamination estimates. It provides the underlying data for taxonomic classification and genome quality metrics in metagenomic and isolate genome analyses. | Biological Sciences |
| chemprop | 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. | Chemical Sciences |
| chemps2 | chemps2 is an open-source software package implementing the Density Matrix Renormalization Group (DMRG) algorithm for quantum chemistry applications. It is designed to efficiently compute accurate electronic structure properties of strongly correlated molecular systems by exploiting matrix product states and operators. | Physical Chemistry |
| chimerax | 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. | Biological Sciences |
| cimfomfa | 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. | |
| cistem | CISTEM is a computational framework designed for the prediction of dual phase RNA secondary structures. | Biological Sciences |
| ckdmip | CKDmip is a software for computing cosmic microwave background (CMB) radiation temperature anisotropies and polarization spectra using the Cosmic Microwave Background (CMB) perturbation code. | Physical Sciences |
| clang | 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. | Computer & Information Sciences |
| clhep | 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. | Physical Sciences |
| climetlab | 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. | Earth & Environmental Sciences |
| clip | 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. | Computer & Information Sciences |
| clp | 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. | Engineering & Technology |
| cmake | 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. | Engineering & Technology |
| coco | COCO (Common Objects in Context) is a large-scale image dataset widely used to train and evaluate computer-vision models for object detection, instance and panoptic segmentation, person keypoint detection, and image captioning. The 2017 release provides roughly 118,000 training, 5,000 validation, and 41,000 test images, annotated with bounding boxes, instance masks, keypoints, and captions across 80 object categories. It is a standard benchmark in the field, with a public evaluation server for the held-out test split. | Applied Computer Science |
| coinutils | 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. | Mathematics |
| colabfold | 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. | Biological Sciences |
| colmap | COLMAP is a general-purpose, open-source Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a focus on ease of use and extensibility. | Computer Science |
| colorize | Ruby gem for colorizing text using ANSI escape sequences. Extends String class or add a ColorizedString with methods to set the text color, background color and text effects. | |
| colossalai | 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. | Computer & Information Sciences |
| conceptual captions 3 million (cc3m) | Conceptual Captions 3 Million (CC3M) is a large-scale dataset designed for training and evaluating image captioning and vision-language models. It contains approximately 3 million image-caption pairs collected from the web, where captions are derived from alt-text descriptions. CC3M is widely used to develop and benchmark models that generate natural language descriptions of images, facilitating research in multimodal machine learning and computer vision. | Artificial Intelligence and Intelligent Systems |
| configurable-http-proxy | A proxy server that allows for configurable routing of HTTP requests, often used in conjunction with JupyterHub and other web applications. | Other Computer and Information Sciences |
| coordgenlibs | 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. | Chemical Sciences |
| cotainr | cotainr is a Python-based user space container builder designed to create Apptainer (formerly Singularity) containers without requiring root privileges. It facilitates building container images in user environments, enabling reproducible and portable HPC and scientific workflows. | Computer Science |
| coverage | Coverage is a tool used to measure the extent to which the source code of a program has been tested. It is often used in software development to assess the quality and thoroughness of testing by determining which parts of the code have been executed during testing. | Engineering & Technology, Computer & Information Sciences, Software Engineering, Systems & Development |
| cp2k | 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. | Physical Sciences |
| cpio | cpio is a general file archiver and compression utility that is used to manage archives of files. It can create, extract, and list the contents of archives in various formats. | Computer Science |
| cppe | CPPE (C++ Polarizable Embedding) is a modern, open-source library designed to facilitate polarizable embedding (PE) calculations in quantum chemistry. It provides an efficient and flexible framework to include environmental effects in electronic structure computations by coupling quantum mechanical methods with classical polarizable models. | Physical Chemistry |
| cppunit | 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. | Computer & Information Sciences |
| cppy | C++ embedded Python library to seamlessly interact with C++ and Python code within the same application. | Computer & Information Sciences |
| crb-blast | crb-blast (Conditional Reciprocal Best BLAST) is a bioinformatics tool implemented in Ruby that identifies orthologous gene pairs between two species by performing conditional reciprocal best BLAST searches. It improves ortholog detection by applying conditional filters to standard reciprocal best hit BLAST results. | Biochemistry and Molecular Biology |
| cryosparc | CryoSPARC is a comprehensive software platform for cryo-EM data processing that enables high-resolution structure determination of biological macromolecules. | Biological Sciences |
| cryptography | 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. | Computer & Information Sciences |
| ctffind | CTFFIND is a widely used software tool for estimating the contrast transfer function (CTF) parameters from electron microscopy images, particularly in cryo-electron microscopy (cryo-EM). It helps determine defocus values and astigmatism parameters critical for high-resolution image reconstruction. | Biophysics |
| cubegui | Cubegui is a graphical user interface (GUI) software designed for visualizing and analyzing volumetric data in computational chemistry and materials science. | Natural Sciences |
| cubelib | cubelib is a C++ library for parallel reduction operations on multi-dimensional arrays using CUDA. | Computer & Information Sciences |
| cubewriter | Cubewriter is a software tool that enables researchers to organize, write, and format scientific papers efficiently. | Other Natural Sciences |
| cuda | 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. | Computer & Information Sciences |
| cuda-python | cuda-python is a Python package that provides bindings to the CUDA API, allowing developers to write Python code that can leverage the power of NVIDIA GPUs for high-performance computing tasks. | Computer Science |
| cuda-samples | 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. | Computer & Information Sciences |
| cuda_python | cuda_python is a Python package that provides Python bindings and APIs to directly access NVIDIA CUDA parallel computation platform and programming model. It enables Python developers to write GPU-accelerated code by interfacing with CUDA runtime and driver APIs, allowing fine-grained control over GPU resources and kernel launches. | Computer Science |
| cudacore | 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. | Engineering & Technology |
| cudf | 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. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| cudnn | 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. | Computer Science |
| cunit | 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. | Computer & Information Sciences |
| cupy | 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. | Computer & Information Sciences |
| curl | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| cusparselt | 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. | Computer & Information Sciences |
| cutadapt | 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. | Biological Sciences |
| cutensor | 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. | Computer & Information Sciences |
| cutlass | CUTLASS (CUDA Templates for Linear Algebra Subroutines and Solvers) is a collection of CUDA C++ templates that facilitate high-performance matrix-multiplication (GEMM) and other linear algebra operations. | Computer Science |
| cython | 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. | Computer & Information Sciences |
| cython-blis | Cython wrapper around BLIS linear algebra library for Python. | Computer & Information Sciences |
| dace | 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. | Computer & Information Sciences |
| dask | 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. | Computer & Information Sciences |
| dask-labextension | Dask Labextension is a JupyterLab extension that provides a graphical interface for Dask, enabling users to manage and visualize Dask clusters and tasks directly from JupyterLab. | Computer Science |
| datamash | Datamash is a command-line program that performs basic numeric, textual, and statistical operations on input data, typically in tabular format. | Data Analysis |
| dataspaces | DataSpaces is a middleware framework designed to enable in-situ and in-transit data sharing and coupling among scientific applications running concurrently on HPC systems. It provides a distributed shared-space abstraction that facilitates asynchronous data exchange, reducing I/O bottlenecks and improving scalability in large-scale simulations and data analytics workflows. | Computer Science |
| dataversioncontrol/dvc | ||
| dav1d | dav1d is a fast and lightweight AV1 video decoder developed by the VideoLAN and FFmpeg communities. It is designed to efficiently decode AV1 video streams on a wide range of devices including low-power embedded systems and high-end desktops, providing high performance and low latency decoding. | Computer Science |
| db | db is a simple and minimalistic database library for Python, designed to provide a lightweight interface for basic database operations. | Computer & Information Sciences, Computer Science |
| db_file | 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. | Computer & Information Sciences |
| dbcsr | 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. | Other Natural Sciences |
| dbus | 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. | Computer & Information Sciences |
| dbus-glib | 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. | Computer & Information Sciences |
| dcmtk | 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. | Medical & Health Sciences |
| deepdiff | DeepDiff is a Python library for deep (nested) comparisons of objects. | Computer & Information Sciences |
| deltalake | Delta Lake is an open-source storage layer that brings reliability to data lakes. It provides ACID transactions, scalable metadata handling, and unifies streaming and batch data processing. | Computer Science |
| dendropy | DendroPy is a flexible and modular phylogenetic computing library in Python, offering reading, writing, simulation, and manipulation of phylogenetic trees and associated data. | Biological Sciences |
| desmond | 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. | Biological Sciences |
| diamond | 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. | Biological Sciences |
| dice | Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems. | |
| dill | 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. | Computer & Information Sciences |
| dm-haiku | dm-haiku is a neural network library built on top of JAX, designed to provide a simple, composable, and flexible interface for building deep learning models. It emphasizes functional programming paradigms and integrates seamlessly with JAX's automatic differentiation and hardware acceleration capabilities. | Artificial Intelligence and Intelligent Systems |
| dm-tree | 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. | Computer & Information Sciences |
| dorado | 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. | Engineering & Technology |
| double-conversion | 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. | Computer & Information Sciences |
| doxygen | 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. | Software Engineering, Systems & Development |
| draco | 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. | Computer & Information Sciences |
| drep | 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. | Biological Sciences |
| dtcmp | dtcmp is a parallel software tool designed for distributed-memory comparison and sorting of data. It provides efficient algorithms for comparing, sorting, and merging large datasets distributed across multiple processors in high-performance computing environments. | Computer Science |
| dulwich | Dulwich is a pure-Python implementation of the Git file formats and protocols. It provides tools and libraries to interact with Git repositories programmatically without requiring the Git command-line tool. Dulwich supports reading and writing Git repositories, handling Git objects, references, and packfiles, and implementing Git client and server protocols. | Software Engineering |
| easybuild | 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. | Engineering & Technology |
| easybuild-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. | Computer & Information Sciences |
| easybuild-aces-myeb | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# | |
| easybuild-aces-scratch | User EasyBuild environment for aces.hprc.tamu.edu in $SCRATCH/eb. Description Source: https://hprc.tamu.edu/software/aces/# | |
| easybuild-aces-tmp | 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. | Engineering & Technology |
| ecbuild | 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. | Earth & Environmental Sciences |
| eccodes | 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. | Earth & Environmental Sciences |
| eggnog-mapper | 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. | Biological Sciences |
| eigen | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. | Computer & Information Sciences |
| einops | 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. | Computer & Information Sciences |
| elfutils | 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. | Other Computer and Information Sciences |
| elpa | 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. | Computer & Information Sciences |
| elsi | ELSI (Electron-Lattice Solvation Interface) is a software package designed for simulating the interaction of electrons with lattice structures in materials science. | Quantum Mechanics |
| emacs | 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. | Computer & Information Sciences |
| enchant-2 | 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. | Computer & Information Sciences |
| entrezdirect | Entrez Direct (EDirect) is a set of UNIX command-line utilities that provide access to the Entrez databases at the National Center for Biotechnology Information (NCBI). It allows users to retrieve, manipulate, and analyze data from various NCBI databases including PubMed, Gene, and Protein. | Bioinformatics |
| esmf | 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. | Physical Sciences |
| exiv2 | 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. | Computer & Information Sciences |
| expat | Expat is an XML parser library written in C. It is a fast and lightweight library that is designed for high-performance applications. | Computer & Information Sciences |
| expect | Expect is a program that "talks" to other interactive programs according to a script. It is used for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. | Other Computer and Information Sciences |
| expecttest | 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. | |
| eztrace | 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. | Computer & Information Sciences |
| fasta | FASTA is a sequence alignment tool that is used for comparing nucleotide or protein sequences to a database of sequences. | Genomics |
| fastahack | fastahack is a small application for indexing and extracting sequences and subsequences from FASTA files. The included Fasta.cpp library provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use. | |
| fastai | 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. | Computer & Information Sciences |
| fastani | 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. | Biological Sciences |
| fastqc | 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. | Biological Sciences |
| fasttext | Amazon Reviews dataset for sentiment analysis | |
| fasttree | 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. | Biological Sciences |
| fds | Fire Dynamics Simulator (FDS) is a computational fluid dynamics (CFD) model designed to simulate fire-driven fluid flow. | Fire Dynamics |
| febio | FEBio (Finite Elements for Biomechanics) is a specialized finite element software suite designed for nonlinear biomechanical simulations. It is tailored to model the mechanical behavior of biological tissues and systems, including soft tissues, bones, and engineered biomaterials, with support for multiphasic and multiphysics phenomena. | Mechanical Engineering |
| fermi-lite | fermi-lite is a lightweight, fast, and memory-efficient de novo assembler for Illumina short reads, designed primarily for assembling small genomes or targeted regions. It implements a succinct data structure and a simplified assembly algorithm to produce contigs quickly with low memory usage. | Biochemistry and Molecular Biology |
| fetk | FETK The Finite Element ToolKit (FETK) is a collaboratively developed, evolving collection of adaptive finite element method (AFEM) software libraries and tools for solving coupled systems of nonlinear geometric partial differential equations (PDE). | |
| ffmpeg | 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. | Computer Science |
| ffnvcodec | ffnvcodec is a codec library provided by NVIDIA for efficient video encoding and decoding using the NVIDIA GPU hardware acceleration. | Computer & Information Sciences |
| fftw | 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. | Mathematics |
| fftw.mpi | 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. | Mathematics |
| fiji | 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. | Other Natural Sciences |
| file | 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. | Software Engineering |
| filevercmp | filevercmp is a utility program used to compare two file version strings and determine their relative ordering. It is commonly used in package management and software distribution systems to sort or compare version numbers that may contain numeric and alphabetic components. | Software Engineering |
| fiona | Fiona is a Python library for reading and writing geospatial vector data formats. | Earth & Environmental Sciences |
| firefox | 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. | Computer & Information Sciences |
| flac | 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. | Other Computer & Information Sciences |
| flann | FLANN (Fast Library for Approximate Nearest Neighbors) is a library for performing fast approximate nearest neighbor searches in high-dimensional spaces. | Artificial Intelligence and Intelligent Systems |
| flash | 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. | Physical Sciences |
| flash-attention | FlashAttention is a highly efficient implementation of the attention mechanism used in transformer models, designed to optimize memory usage and speed, particularly for large-scale models. | Artificial Intelligence and Intelligent Systems |
| flask | 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. | Computer & Information Sciences |
| flatbuffers | 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. | Computer & Information Sciences |
| flatbuffers-python | FlatBuffers is a serialization library that allows you to read and write structured data efficiently. The Python implementation provides bindings to work with FlatBuffers in Python applications. | Computer and Information Sciences |
| flex | 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. | Other Computer and Information Sciences |
| flexiblas | 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. | Other Mathematics |
| flit | Flit is a simple tool for building and distributing Python packages. | Computer & Information Sciences |
| flit-core | ||
| flook | The fortran-Lua-hook library. It allows abstraction of input files to be pure Lua files to enable configuration of internal variables through an embedded Lua interpreter. Any valid Lua script can be executed from within any fortran application at points where the application creates Lua channels. Its main usage is the ability to change run-time variables at run-time in order to optimize, or even change, the execution path of the parent program. | |
| fltk | 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. | Engineering & Technology |
| fmt | fmt is a modern formatting library for C++ that provides a safe and easy way to format strings. | Other Computer and Information Sciences |
| fontconfig | 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. | Engineering & Technology |
| fonttools | FontTools is a library for manipulating font files, primarily TrueType and OpenType fonts. It allows for the extraction, modification, and creation of font files. | Other Computer and Information Sciences |
| foss | 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. | Other Computer & Information Sciences |
| fosscuda | 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. | Computer & Information Sciences |
| freebayes | 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. | Biological Sciences |
| freeglut | 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. | Computer & Information Sciences |
| freeimage | FreeImage is an open-source graphics library that supports popular image formats and features image loading, saving, conversion, manipulation, and processing capabilities. | Engineering & Technology |
| freesasa | ||
| freetype | 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. | Computer & Information Sciences |
| freexl | 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. | Computer & Information Sciences |
| fribidi | GNU FriBidi is an implementation of the Unicode Bidirectional Algorithm (bidi). It also provides utility functions to help work with bidirectional text. | Computer & Information Sciences |
| fsom | fsom is a tiny C library designed for managing Self-Organizing Maps (SOM) neural networks. It provides basic functionalities to create, train, and use SOMs for unsupervised learning tasks. | Artificial Intelligence and Intelligent Systems |
| g2clib | 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. | Earth & Environmental Sciences |
| g2lib | 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. | Computer & Information Sciences |
| gatb-core | GATB-core is a library designed for high-performance bioinformatics applications, particularly for genome assembly and analysis. | Genomics |
| gatk | 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. | Biological Sciences |
| gc | GC is a compiler for the Go programming language. | Computer & Information Sciences, Computer Science |
| gcc | 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. | Computer Science |
| gcccore | 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. | Computer & Information Sciences, Software Engineering, Systems & Development |
| gcccuda | 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. | Computer & Information Sciences |
| gcloud | gcloud is a command-line interface for Google Cloud Platform, enabling users to manage resources and applications hosted on Google Cloud. | Computer Science |
| gconf | 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. | Computer & Information Sciences |
| gdal | 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. | Earth & Environmental Sciences, Engineering & Technology |
| gdb | 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. | Computer & Information Sciences |
| gdk-pixbuf | 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. | Computer & Information Sciences |
| gdown | gdown is a command-line utility that allows users to download files from Google Drive, particularly files that are too large for direct download links. | Computer Science |
| gdrcopy | 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. | Computer & Information Sciences |
| geant4 | 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. | Physical Sciences |
| geant4-data | Datasets for Geant4. | |
| gemmi | ||
| generativemodels | 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. | |
| genomepy | 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. | Biological Sciences |
| geocube | 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. | Physical Sciences |
| geopandas | Geopandas is an open-source python library for working with geospatial data, enabling users to easily manipulate and analyze geospatial datasets. | Earth & Environmental Sciences |
| geos | 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. | Computer & Information Sciences |
| gettext | 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. | Computer & Information Sciences |
| gfbf | 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. | Computer & Information Sciences |
| gflags | gflags is a library that implements commandline flags processing in C++. It provides a simple way to define and parse command-line flags, making it easier to handle user input in command-line applications. | Other Computer and Information Sciences |
| ghostscript | 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. | Computer & Information Sciences, Engineering & Technology |
| giflib | 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. | Computer Science |
| gigatoken | gigatoken is a high-performance tokenizer library designed for language model tokenization at gigabytes per second speeds. It is implemented in Rust and optimized for fast and efficient tokenization of text documents, supporting various language models. | Artificial Intelligence and Intelligent Systems |
| git | 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. | Computer & Information Sciences, Software Engineering, Systems & Development |
| git-lfs | 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. | Engineering & Technology |
| gitpython | 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. | Computer Science |
| gklib | gklib is a C++ library for geometric kernels that provides efficient and accurate geometric algorithms for computational geometry and related fields. | Mathematics |
| gklib-metis | gklib-metis is a software library that provides graph partitioning and mesh partitioning algorithms, integrating the capabilities of the METIS library with the GKlib framework for efficient graph and mesh processing. | Applied Mathematics |
| gl2ps | 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. | Computer Science |
| glew | 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. | Computer Science |
| glfw | 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. | Computer & Information Sciences |
| glib | 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. | Computer & Information Sciences |
| glib-networking | 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. | Computer & Information Sciences |
| glm | glm is a Python library for Generalized Linear Models (GLM) with support for exponential family distributions. | Mathematics |
| globalarrays | Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model | |
| globus-cli | 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. | Other Computer & Information Sciences |
| glog | glog is a C++ library that implements a logging framework designed to provide a simple and efficient way to log messages from applications. | Software Engineering |
| glpk | 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. | Mathematics |
| glslang-spirv | Glslang is the official reference compiler front end for the OpenGL ES and OpenGL shading languages. It implements a strict interpretation of the specifications for these languages. It is open and free for anyone to use, either from a command line or programmatically. The OpenGL and OpenGL ES working groups are committed to maintaining consistency between the reference compiler and the corresponding shading language specifications. | |
| gmap-gsnap | 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. | Biological Sciences |
| gmp | 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. | Mathematics |
| gmpy2 | 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. | Computer & Information Sciences |
| gnuplot | 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. | Physical Sciences |
| gnutls | GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols, providing various cryptographic algorithms. | Computer & Information Sciences |
| go | Go is an open-source programming language designed for simplicity and efficiency, particularly in systems programming and web development. | Computer Science |
| gobject-introspection | 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. | Computer & Information Sciences |
| gomkl | GOMKL is a library that provides optimized mathematical routines for high-performance computing applications, particularly those that require linear algebra operations. | Mathematics |
| gompi | 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. | Engineering & Technology |
| gompic | 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. | Physical Sciences |
| googlebenchmark | Google Benchmark is a microbenchmark support library designed to measure and report the performance of small code snippets in C++. It provides a framework for writing benchmarks, running them with various configurations, and producing detailed performance reports. | Software Engineering, and Development |
| googletest | 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. | Computer & Information Sciences |
| gotranseq | gotranseq is a command-line tool designed for translating nucleotide sequences into protein sequences using the genetic code. It supports multiple translation tables and can process sequences in various formats, making it useful for bioinformatics workflows involving sequence analysis and annotation. | Biochemistry and Molecular Biology |
| gpaw | 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. | Physical Sciences |
| gpaw-setups | gpaw-setups is a collection of atomic datasets (setups) used by the GPAW code, a grid-based projector-augmented wave (PAW) method for electronic structure calculations within density functional theory (DFT). These setups define the atomic potentials and basis information necessary for accurate and efficient simulations of materials and molecules. | Condensed Matter Physics |
| gperf | 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. | Computer & Information Sciences |
| gperftools | 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. | Engineering & Technology |
| gpflow | 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. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| gpgme | GPGME (GnuPG Made Easy) is a C library that allows the use of GnuPG (GNU Privacy Guard) for encryption and signing of data and communications. It provides a high-level interface to GnuPG, making it easier to integrate cryptographic functions into applications. | Computer Science |
| gpustat | 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. | Engineering & Technology |
| gpytorch | 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. | Computer & Information Sciences |
| graphblas | GraphBLAS is a collection of high-performance linear algebraic operations specifically designed for sparse graphs and matrices. | Computer & Information Sciences |
| graphene | Graphene is a Python library for building GraphQL APIs fast and easily. | Computer & Information Sciences |
| graphicsmagick | 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. | Other Computer & Information Sciences |
| graphite2 | 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. | Computer & Information Sciences |
| graphviz | Graphviz is open source graph visualization software. It is used for creating structured diagrams such as flowcharts, network diagrams, and more. | Computer & Information Sciences |
| graphviz-python | 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. | Computer & Information Sciences |
| grass | GRASS GIS (Geographic Resources Analysis Support System) is a free and open source Geographic Information System (GIS) software suite used for geospatial data management, analysis, image processing, spatial modeling, and visualization. It supports raster, vector, and geospatial database formats and provides a wide range of tools for environmental and earth sciences research. | Earth and Environmental Sciences |
| great_tables | great_tables is a Python library designed to simplify the creation, manipulation, and visualization of complex tables and data frames. It provides an intuitive API for generating richly formatted tables that can be exported to multiple formats including HTML, LaTeX, and Markdown. | Software Engineering, Systems, and Development |
| greenlet | 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. | Computer & Information Sciences |
| groff | 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. | Computer & Information Sciences |
| gromacs | 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. | Biological Sciences |
| grpcio | gRPC is a high-performance, open-source universal RPC framework that leverages HTTP/2 for transport, Protocol Buffers as the interface description language, and it provides features such as authentication, load balancing, and more. | Computer Science |
| gsl | 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. | Other Mathematics |
| gslib | gslib is an open-source and free collection of Fortran 77 subroutines for geostatistical applications. | Earth & Environmental Sciences |
| gst-plugins-bad | 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. | Computer & Information Sciences |
| gst-plugins-base | 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. | Computer & Information Sciences |
| gstreamer | 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. | Computer & Information Sciences |
| gtdb-tk | GTDB-Tk is a toolkit for the classification of genomes into the Genome Taxonomy Database (GTDB) framework, providing tools for taxonomic classification and phylogenetic analysis of microbial genomes. | Microbial Ecology |
| gtk2 | 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. | Computer & Information Sciences |
| gtk3 | 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. | Computer & Information Sciences |
| gtk4 | 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. | Computer & Information Sciences |
| gts | 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. | Computer & Information Sciences |
| guile | 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. | Computer & Information Sciences |
| gymnasium | Gymnasium is a Python library which provides tools and utilities for creating and manipulating complex mathematical expressions and equations. | Mathematics |
| gzip | 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. | Engineering & Technology |
| h5py | 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. | Computer & Information Sciences |
| harfbuzz | 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. | Computer & Information Sciences |
| hatch-jupyter-builder | hatch-jupyter-builder is a plugin for the Hatch Python packaging tool that enables building Jupyter Notebook extensions and distributing them as part of Python packages. It automates the process of bundling Jupyter notebooks, extensions, and related assets into distributable Python packages, facilitating reproducible research and sharing of notebook-based projects. | Software Engineering, Systems, and Development |
| hatchling | 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. | Biological Sciences |
| hdf | 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. | Other Computer & Information Sciences |
| hdf-eos | 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. | Physical Sciences |
| hdf-eos5 | 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. | Natural Sciences |
| hdf5 | 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. | Computer Science |
| heffte | HeFFTe is a high-performance Fast Fourier Transform (FFT) library designed for distributed memory systems. It leverages advanced algorithms to optimize FFT computations on large datasets, making it suitable for scientific computing applications. | Numerical Analysis |
| help2man | help2man is a tool that can generate simple man pages from the '--help' and '--version' output of other commands. | Engineering & Technology |
| hf-datasets | hf-datasets is a Python library developed by Hugging Face that provides easy access to a wide variety of datasets for machine learning and natural language processing tasks. It offers a simple API to load, preprocess, and share datasets, facilitating reproducible research and rapid prototyping. | Artificial Intelligence and Intelligent Systems |
| hh-suite | 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. | Biological Sciences |
| highway | 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. | Biological Sciences |
| hipify | Hipify is a tool that converts CUDA code to HIP (Heterogeneous-compute Interface for Portability) code, allowing developers to port their applications from NVIDIA GPUs to AMD GPUs. | Software Engineering |
| hiredis | 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. | Computer & Information Sciences |
| hisat2 | 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. | Biological Sciences |
| hmmer | 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. | Biological Sciences |
| horovod | 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. | Computer & Information Sciences |
| hpc-x | 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. | Engineering & Technology |
| hpl | 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. | Engineering & Technology |
| hprc_utils | hprc_utils is a collection of utility tools for managing and analyzing High Performance Computing (HPC) environments and workflows. | Engineering & Technology |
| htseq | 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. | Biological Sciences |
| htslib | 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. | Biological Sciences |
| httpx | ||
| huggingface-hub | ||
| huggingface_hub | The Hugging Face Hub is a platform for sharing and discovering machine learning models and datasets. It provides tools for model versioning, collaboration, and integration with various machine learning frameworks. | Natural Language Processing |
| humann | 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. | Biological Sciences |
| hunspell | Hunspell is a spell checker and morphological analyzer software designed for languages with rich morphology and complex word compounding. | Other Computer & Information Sciences |
| hwloc | 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. | Computer & Information Sciences |
| hydra | Hydra is an open-source framework for elegantly configuring complex applications, primarily in Python. It enables users to compose and override hierarchical configurations dynamically through config files and command-line arguments, facilitating flexible experimentation and reproducibility in research and development. | Software Engineering, and Development |
| hyperopt | 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. | Computer & Information Sciences |
| hypothesis | 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. | Computer & Information Sciences |
| hypre | 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. | Mathematics |
| iccifort | 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. | Engineering & Technology |
| icon | ICON is a flexible, scalable, high-performance modelling framework for weather, climate and environmental prediction that provides actionable information for society and advances our understanding of the Earth's climate system. | |
| icu | 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. | Computer & Information Sciences |
| igprof | 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. | Engineering & Technology |
| iimpi | 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. | Biological Sciences |
| ijulia | iJulia is an interactive notebook interface for the Julia programming language, enabling users to create and share documents that contain live code, equations, visualizations, and narrative text. | Data Science |
| imageio | 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. | Computer & Information Sciences |
| imagej | 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. | Biochemistry and Molecular Biology |
| imagemagick | ImageMagick is a free and open-source software suite for creating, editing, composing, or converting bitmap images. | Computer & Information Sciences |
| imagenet | Imagenet is a large-scale visual database designed for use in visual object recognition research. It is widely used as a benchmark dataset for training and evaluating deep learning models, especially convolutional neural networks (CNNs). Various software implementations and utilities exist to facilitate downloading, preprocessing, training, and evaluating models on the ImageNet dataset. | Artificial Intelligence and Intelligent Systems |
| imake | 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. | Engineering & Technology |
| imath | 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 |
| imbalanced-learn | 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. | Computer & Information Sciences |
| imkl | imkl is a open-source software library for creating and managing knowledge graphs for various applications in artificial intelligence, data science, and information retrieval. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| imkl-fftw | 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. | Mathematics |
| iml | Interpretable Machine Learning | Computer & Information Sciences |
| impi | impi is a high-performance message passing library that provides asynchronous messaging and queuing functionalities for parallel computing applications. | Engineering & Technology |
| infernal | 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. | Biological Sciences |
| intel compiler | 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. | Computer & Information Sciences |
| intel-compilers | Intel Compilers are a suite of optimizing compilers for C, C++, and Fortran programming languages, designed to enhance performance on Intel architectures. | Software Engineering |
| intel/aikit | ||
| intelclusterchecker | Intel® Cluster Checker verifies the configuration and performance of Linux* OS-based clusters. Anomalies and performance differences can be identified and practical resolutions provided. | |
| intelpython | This is the Intel Python distribution. | |
| intervaltree | A Python library for creating and manipulating interval trees, which are useful for storing intervals and performing efficient queries on them. | Computer Science |
| intltool | Intltool is a set of tools to centralize translation of many different file formats using a single language-styled file. | Computer & Information Sciences |
| ipython | 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. | Computer & Information Sciences |
| iq-tree | 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. | Biological Sciences |
| irkernel | IRkernel is a kernel for the R programming language that allows users to run R code in Jupyter notebooks, providing an interactive computing environment. | Statistics and Probability |
| isa-l | 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. | Engineering & Technology |
| isl | 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. | Computer & Information Sciences |
| itk | 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. | Engineering & Technology |
| jansson | 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. | Computer & Information Sciences |
| jasper | 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. | Computer & Information Sciences |
| java | 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. | Computer & Information Sciences |
| jax | JAX is an open-source software library for high-performance machine learning research, particularly for automatic differentiation, and numerical and scientific computing. | Computer & Information Sciences |
| jbigkit | jbigkit is a software library for encoding and decoding images in the JBIG format, which is particularly efficient for bi-level images such as scanned documents. | Other Computer and Information Sciences |
| jedi | jedi is a static analysis tool for Python that is typically used in IDEs/editors plugins. Jedi has a focus on autocompletion and goto functionality. Other features include refactoring, code search and finding references. | |
| jellyfish | 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. | Biological Sciences |
| jemalloc | 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. | Computer & Information Sciences |
| jmol | Jmol is an open-source Java viewer for chemical structures in 3D with features for visualization, analysis, and manipulation of molecular structures. | Chemical Sciences |
| json-c | 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. | Computer & Information Sciences |
| json-fortran | json-fortran is a Fortran library for reading and writing JSON data. It provides a simple interface for working with JSON in Fortran applications, allowing users to easily serialize and deserialize data structures. | Software Engineering |
| jsoncpp | JsonCpp is a C++ library that allows manipulating JSON data structures. It provides features for parsing, generating, and manipulating JSON data in C++ applications. | Computer & Information Sciences |
| judy | Judy is a C library that provides a collection of functions to efficiently manage data arrays to store and retrieve key/value pairs. | Other Computer & Information Sciences |
| julia | 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. | Computer & Information Sciences |
| julia_tamu | Julia is a high-level, high-performance dynamic programming language for numerical computing. | |
| jupyter-bundle | jupyter-bundle is a JupyterLab extension developed by Daipe that provides bundling capabilities within JupyterLab environments. It enables users to package notebooks and related resources efficiently, facilitating export and integration workflows. | Computer Science |
| jupyter-resource-usage | A Jupyter Notebook extension that provides resource usage statistics for notebooks, including CPU and memory usage. | Computer Science |
| jupyter-server | 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. | Computer & Information Sciences |
| jupyter-server-proxy | A Jupyter server extension that allows users to create proxies for other web services, enabling them to be accessed through Jupyter notebooks. | Computer Science |
| jupyterhub | 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. | Computer & Information Sciences |
| jupyterlab | 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. | Computer & Information Sciences |
| jupyterlmod | 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. | Other Natural Sciences |
| jupyternotebook | Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations, and narrative text. | Computer Science |
| kaggle | Kaggle is an online platform for data science competitions, datasets, and collaborative projects. It provides tools and environments for data scientists and machine learning practitioners to develop, share, and deploy models and analyses. | Artificial Intelligence and Intelligent Systems |
| kahip | 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. | Computer & Information Sciences |
| kaleido | Kaleido is a high-performance image export engine for Plotly, enabling the generation of static images from interactive visualizations. | Computer Science |
| kalign | 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. | Biological Sciences |
| kallisto | 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. | Biological Sciences |
| kblas-gpu | 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. | Engineering & Technology |
| keras | 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. | Computer & Information Sciences |
| kim-api | 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. | Physical Sciences |
| kineto | 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. | Engineering & Technology |
| kmcp | kmcp is a fast and accurate metagenomic profiling tool designed for taxonomic classification of microbial communities from shotgun sequencing data. It leverages k-mer based indexing and pseudo-mapping techniques to efficiently identify and quantify species present in metagenomic samples. | Biological Sciences |
| kokkos | 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. | Computer & Information Sciences |
| kraken2 | Kraken 2 is a taxonomic sequence classifier that assigns taxonomic labels to short DNA sequences, such as those generated by high-throughput sequencing technologies. | Metagenomics |
| lame | 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. | Other Engineering & Technologies |
| lammps | 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. | Chemical Sciences |
| lasso-python | 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. | Mathematics |
| learnmsa | learnMSA is a computational tool designed for learning and aligning large protein families by leveraging protein language models. It integrates machine learning techniques to improve multiple sequence alignment (MSA) quality for large-scale protein datasets. | Biochemistry and Molecular Biology |
| leptonica | 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. | Computer & Information Sciences |
| lerc | 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. | Other Natural Sciences |
| leveldb | 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. | Computer & Information Sciences |
| levenshtein | ||
| levmar | Levmar is a library for solving non-linear least squares problems using the Levenberg-Marquardt algorithm. | Other Mathematics |
| libaec | libaec is a C library for lossless image compression. | Computer & Information Sciences |
| libaio | 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. | Computer & Information Sciences |
| libaom | libaom is the official AOMedia video codec library for AV1. It provides the tools necessary for encoding and decoding AV1 video streams, offering a royalty-free alternative to other codecs with improved compression efficiency. | |
| libarchive | 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++. | Computer & Information Sciences |
| libassuan | libassuan is a library that provides a simple and secure way to handle IPC (Inter-Process Communication) between applications, primarily used in the context of GnuPG. | Computer Science |
| libatomic_ops | 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. | Computer & Information Sciences |
| libcerf | 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. | Mathematics |
| libcint | libcint is an open source library for analytical Gaussian integrals. It provides C/Fortran API to evaluate one-electron / two-electron integrals for Cartesian / real-spheric / spinor Gaussian type functions. | |
| libcircle | libcircle is a library designed for parallel programming in C and C++ that simplifies the development of distributed applications. It provides a high-level API for managing communication between processes in a cluster environment. | Computer Science |
| libclc | libclc is an open source implementation of the library requirements of the OpenCL C programming language, as specified by the OpenCL 1.1. | |
| libdap | 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. | Other Computer & Information Sciences |
| libde265 | libde265 is an open-source implementation of the H.265 (HEVC) video codec, designed for efficient video compression and decompression. | Computer Science |
| libdeflate | libdeflate is a library for fast, flexible, and memory-efficient DEFLATE-based compressed data decompression. | Computer & Information Sciences |
| libdivsufsort | libdivsufsort is a library for constructing suffix arrays and related data structures efficiently. | Computer Science |
| libdrm | Direct Rendering Manager (DRM) library for interacting with kernel mode-setting (KMS) drivers, particularly the Direct Rendering Infrastructure (DRI) modules in the Linux kernel. | Computer Science |
| libepoxy | 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. | Computer & Information Sciences |
| libev | 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. | Computer & Information Sciences |
| libevent | 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. | Computer & Information Sciences |
| libfabric | 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. | Engineering & Technology |
| libfdf | LibFDF is the official implementation of the FDF specifications for use in client codes. At present the FDF format is used extensively by Siesta, and it has been an inspiration for several other code-specific input formats. | |
| libffi | 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. | Computer & Information Sciences |
| libfyaml | libfyaml is a C library for parsing and emitting YAML, designed to be fast and simple to use. | Other Computer and Information Sciences |
| libgcrypt | Libgcrypt is a general-purpose cryptographic library originally based on code from GnuPG. It provides various cryptographic algorithms to secure data and communications. | Computer & Information Sciences |
| libgd | 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. | Other Computer & Information Sciences |
| libgeotiff | Libgeotiff is a library for reading and writing coordinate system information embedded in geotiff files. | Earth & Environmental Sciences |
| libgit2 | 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. | Computer & Information Sciences |
| libglu | 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. | Computer & Information Sciences |
| libglvnd | 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. | Computer & Information Sciences |
| libgpg-error | Libgpg-error is a small library that defines common error values for all GnuPG components. It is used by GnuPG and some other packages. | Computer & Information Sciences |
| libgpuarray | 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. | Computer & Information Sciences |
| libgridxc | libgridxc is a library for evaluating exchange-correlation functionals in density functional theory (DFT) calculations. | Computational Chemistry |
| libheif | libheif is a library for reading and writing High Efficiency Image File Format (HEIF) files, which are used for storing images and image sequences. | Computer and Information Sciences |
| libiconv | libiconv is a library that provides character set conversion support. It converts text data between different character encoding schemes. | Computer & Information Sciences |
| libidn | 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). | Computer & Information Sciences |
| libidn2 | Libidn2 is a library that implements the Stringprep, Punycode and IDNA specifications defined by the IETF Internationalized Domain Names (IDN) working group. | Computer & Information Sciences |
| libint | 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. | Chemical Sciences |
| libjpeg-turbo | 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. | Computer & Information Sciences |
| libmad | libmad is a high-quality MPEG audio decoder library that is designed to decode MP3 audio streams efficiently and accurately. | Other Computer and Information Sciences |
| libnsl | 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. | Computer & Information Sciences |
| libogg | Libogg is a reference implementation of the Ogg bitstream format. It provides a simple, low-level API for working with Ogg bitstreams. | Computer & Information Sciences |
| libopus | 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. | Engineering & Technology |
| libpciaccess | 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. | Computer & Information Sciences |
| libpng | 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. | Computer & Information Sciences |
| libpressio | libpressio is a library designed for compressing and decompressing data in scientific computing applications. It provides a flexible framework for integrating various compression algorithms and allows users to easily switch between them. | Computer Science |
| libpsl | 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. | Computer & Information Sciences |
| libpsml | The software library libPSML can be used by electronic structure codes to transparently extract the information in a PSML file and adapt it to their own data structures, or to create converters for other formats. | |
| libreadline | 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. | Computer & Information Sciences |
| librom | 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. | Engineering & Technology |
| librosa | Librosa is a Python package for music and audio analysis. It provides the building blocks necessary to create music information retrieval systems. | Applied Computer Science |
| librsvg | Librsvg is a free software library to render SVG files and convert them to other formats using the Cairo rendering engine. | Computer & Information Sciences |
| librttopo | librttopo is a tool for computational topology focusing on persistent homology and topological data analysis. | Mathematics |
| libseccomp | 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. | Computer & Information Sciences |
| libsharp2 | libsharp2 is a library designed for efficient spherical harmonic transforms and related operations, primarily used in cosmology and astrophysics. | Astrophysics |
| libsndfile | libsndfile is a C library for reading and writing files containing sampled sound (such as WAV, AIFF, and AU) through one standard interface. | Other Natural Sciences |
| libsodium | 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. | Computer & Information Sciences |
| libsoup | 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. | Computer & Information Sciences |
| libspatialindex | 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. | Computer & Information Sciences |
| libspatialite | 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. | Computer & Information Sciences |
| libstdcompat | LibStdCompat is a set of compatibility headers for C++ 14, 17, and 20 for C++11. It aims to be lighter weight and more narrowly tailored than some other alternatives such as Boost or replacing your standard library with libcxx when certain fewer features are needed. | |
| libtasn1 | 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. | Computer & Information Sciences |
| libtiff | 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. | Computer & Information Sciences |
| libtirpc | libtirpc is an open-source library that provides an implementation of Sun's Transport-Independent RPC (TI-RPC) protocol. | Computer & Information Sciences |
| libtommath | libtommath is a free open-source multiple-precision integer library written in C. It is designed for high-performance arithmetic operations on large integers, making it suitable for cryptographic applications and other mathematical computations. | Other Mathematics |
| libtool | Libtool is a generic library support script that manages the creation of static and dynamic libraries on various Unix-like operating systems. | Engineering & Technology |
| libunistring | libunistring is a C library that provides functions to manipulate Unicode strings and includes functions for encoding conversion, case mapping, normalization, and more. | Computer & Information Sciences |
| libunwind | 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. | Engineering & Technology |
| libvdwxc | libvdwxc is a library for the evaluation of van der Waals exchange-correlation functionals in density functional theory calculations. | Quantum Chemistry |
| libvorbis | 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. | Engineering & Technology |
| libvori | libvori is a library for calculating voronoi diagrams. It provides functions for generating voronoi diagrams from a set of points in the plane. | Mathematics |
| libvpx | libvpx is a free software video codec library from Google and the Alliance for Open Media (AOMedia). It serves as the reference software implementation for the VP8 and VP9 video coding formats, and for AV1 a special fork named libaom that was stripped of backwards compatibility. | |
| libwebp | 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. | Other Computer & Information Sciences |
| libwpe | libwpe is a library that provides web platform support for Wayland compositors and other clients that need web content rendered on a Wayland surface. | Computer & Information Sciences |
| libxc | LibXC is a library of exchange-correlation functionals for density-functional theory. | Chemical Sciences |
| libxml2 | 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. | Computer & Information Sciences |
| libxslt | 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. | Computer & Information Sciences |
| libxsmm | 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. | Computer & Information Sciences |
| libyaml | 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. | Computer & Information Sciences, Engineering & Technology |
| libzip | libzip is a C library for reading, creating, and modifying zip archives. It provides a simple programming interface for managing zip files. | Computer & Information Sciences |
| lifelines | 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. | Statistics & Probability |
| lightgbm | ||
| lightning | ||
| likwid | 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. | Engineering & Technology |
| lit | lit is a lightweight, portable, and extensible test runner used primarily for running LLVM-style test suites. It is designed to execute tests, verify outputs, and report results in a structured and flexible manner. | Software Engineering, and Development |
| littlecms | 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. | Computer & Information Sciences |
| llava-onevision | A dataset used for the training of the LLaVA-OneVision model. | |
| llvm | 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. | Computer & Information Sciences |
| llvm-compilers | The LLVM Project is a collection of modular and reusable compiler and toolchain technologies. | |
| lmdb | 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. | Computer & Information Sciences |
| lmod | 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. | Engineering & Technology |
| longranger | Long Ranger is a software package developed by 10x Genomics for analyzing genomic data generated by their Chromium platform. It is specifically designed for processing and analyzing linked-read sequencing data, enabling users to perform tasks such as variant calling and structural variant detection. | Genomics |
| lpsolve | lpsolve is a free linear programming solver based on the revised simplex method. It can solve linear, mixed integer, and quadratic programming problems. | Applied Mathematics |
| lsd2 | Least-squares methods to estimate rates and dates from phylogenies. | |
| lua | 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. | Computer & Information Sciences |
| lwgrp | The light-weight group library defines data structures and collective operations to group MPI processes as an ordered set. Such groups are useful as substitutes for MPI communicators when the overhead of communicator creation is too costly. For example, certain sorting algorithms recursively divide processes into subgroups as the sort algorithm progresses. These groups may be different with each invocation, so that it is inefficient to create and destroy communicators during the sort routine. | |
| lxml | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| lz4 | 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. | Computer & Information Sciences |
| lzo | 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. | Computer & Information Sciences |
| m4 | 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. | Computer & Information Sciences |
| macs2 | 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. | Biological Sciences |
| maeparser | 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. | Chemical Sciences |
| mafft | 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. | Biological Sciences |
| magics | 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. | Earth & Environmental Sciences |
| magma | 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 |
| make | 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. | Engineering & Technology |
| makedepend | 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. | Engineering & Technology |
| makeinfo | 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. | Other Computer & Information Sciences |
| mako | Mako is a template library written in Python. It provides a familiar, non-XML syntax that compiles into Python modules for maximum performance. | Computer & Information Sciences |
| mamba | 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. | Engineering & Technology |
| margo | Margo combines Mercury and Argobots to simplify development of distributed services. Mercury operations are presented as conventional blocking operations, and RPC handlers are presented as sequential threads. This configuration enables high degree of concurrency while hiding the complexity associated with asynchronous communication progress and callback management. | |
| mariadb | 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. | Computer & Information Sciences |
| marimo | ||
| markdown | Markdown is a lightweight markup language with plain-text formatting syntax. Its design allows it to be converted to many output formats, but it is most commonly used for formatting readme files, for writing messages in online discussion forums, and for creating rich text using a plain text editor. | Other Computer and Information Sciences |
| mash | 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. | Biological Sciences |
| matio | 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. | Mathematics |
| matlab | 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. | Mathematics, Applied Mathematics |
| matplotlib | 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. | Computer & Information Sciences |
| maturin | 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. | Computer & Information Sciences |
| maven | 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. | Computer & Information Sciences |
| mayavi | Mayavi is a scientific data visualization tool that integrates seamlessly with Python, providing a powerful interface for 3D visualization of data. | Computer Science |
| mcr | mcr is a computational software used for solving complex mathematical problems and conducting numerical simulations. It provides a high-performance computing environment for researchers and scientists to analyze, model, and solve mathematical equations and algorithms. | Mathematics |
| mctc-lib | Fortran library providing unified molecular structure data handling and geometry file format I/O for computational chemistry applications. The library supports reading and writing of molecular structures in more than twelve different geometry formats and provides element data and coordination number utilities. | |
| mdi | The MolSSI Driver Interface (MDI) project provides a standardized API for fast, on-the-fly communication between computational chemistry codes. This greatly simplifies the process of implementing methods that require the cooperation of multiple software packages and enables developers to write a single implementation that works across many different codes. The API is sufficiently general to support a wide variety of techniques, including QM/MM, ab initio MD, machine learning, advanced sampling, and path integral MD, while also being straightforwardly extensible. Communication between codes is handled by the MDI Library, which enables tight coupling between codes using either the MPI or TCP/IP methods. | |
| mdtraj | MDTraj is a Python library that allows users to analyze molecular dynamics trajectories. It provides tools to read, write, and manipulate trajectory data from various simulation packages. | Biochemistry and Molecular Biology |
| meamfit2 | ||
| memoryviewer | 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. | Computer & Information Sciences |
| mercurial | Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an intuitive interface. | Computer & Information Sciences |
| mercury | Mercury is an RPC framework specifically designed for use in HPC systems that allows asynchronous transfer of parameters and execution requests, as well as direct support of large data arguments. The network implementation is abstracted, allowing easy porting to future systems and efficient use of existing native transport mechanisms. Mercury's interface is generic and allows any function call to be serialized. Mercury is a core component of the Mochi ecosystem of microservices. | |
| mesa | Mesa is an open-source agent-based modeling framework that allows users to create and analyze computational models of complex adaptive systems. | Computer & Information Sciences |
| meson | Meson is an open-source build system meant to be both extremely fast and as user-friendly as possible. | Computer & Information Sciences |
| meson-python | 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. | Computer & Information Sciences |
| metaeuk | MetaEuk is a software tool designed for the identification and annotation of eukaryotic genes from metagenomic data. It utilizes a combination of sequence alignment and machine learning techniques to improve the accuracy of gene predictions in complex environmental samples. | Computational Biology |
| metaphlan | 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. | Biological Sciences |
| methscan | A command line tool for Single-Cell Analysis of Methylation data | |
| metis | 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. | Computer & Information Sciences |
| mfem | 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. | Engineering & Technology |
| mfqe | extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names. | |
| mgard | MGARD is a software package designed for high-performance data compression, particularly for scientific data. It utilizes multigrid techniques to achieve efficient compression rates while maintaining data integrity. | Data Compression Techniques |
| micromamba | micromamba is a lightweight, fast, and flexible package manager for managing environments and packages in Python and other languages. It is designed to be a minimalistic alternative to conda, providing the same functionality with a smaller footprint. | Software Engineering |
| miniconda3 | 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. | Computer & Information Sciences |
| miniforge3 | Miniforge is a community-driven minimal installer for Conda, designed to provide a lightweight and flexible environment for managing packages and environments in Python and other languages. | Biological Sciences |
| minimap2 | 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. | Biological Sciences |
| miniprot | 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. | Biological Sciences |
| minizip | 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. | Software Engineering |
| minpath | MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. | |
| ml-collections | A library that provides a collection of utilities for managing configurations in machine learning projects. | Artificial Intelligence and Intelligent Systems |
| ml_dtypes | ml_dtypes is a stand-alone implementation of several NumPy dtype extensions used in machine learning libraries, including: bfloat16: an alternative to the standard float16 format float8_*: several experimental 8-bit floating point representations including: float8_e4m3b11fnuz float8_e4m3fn float8_e4m3fnuz float8_e5m2 float8_e5m2fnuz | |
| mmg | MMG is a software package designed for the generation and adaptation of unstructured meshes in two and three dimensions. It is particularly useful for numerical simulations in scientific computing. | Computational Science |
| mmseqs2 | 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. | Biological Sciences |
| mmseqs2-gpu | MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. | |
| moab | MOAB (Mesh Oriented datABase) is a software library designed for managing and manipulating unstructured mesh data in high-performance computing applications. | Computational Chemistry |
| modulair | ModuLair is a Python Virtual Environment management tool written by TAMU HPRC. | |
| modular | The Modular command-line interface. | |
| mold | 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. | Biological Sciences |
| monai | 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. | Engineering & Technology |
| motif | 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. | Biological Sciences |
| mpc | 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. | Computer & Information Sciences |
| mpfr | 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. | Mathematics |
| mpi4py | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| mpich | 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. | Computer & Information Sciences |
| mpifileutils | A collection of utilities for managing files in parallel using MPI. | Computer Science |
| mrcfile | mrcfile is a Python library for reading and writing MRC (Medical Research Council) format files, commonly used in electron microscopy and other scientific imaging applications. | Biological Sciences |
| mstore | Molecular structure store for testing. | |
| mujoco | 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. | Engineering & Technology |
| multichoose | 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. | Mathematics |
| multiprocess | multiprocess is a fork of multiprocessing. multiprocess extends multiprocessing to provide enhanced serialization, using dill. multiprocess leverages multiprocessing to support the spawning of processes using the API of the Python standard library's threading module. multiprocessing has been distributed as part of the standard library since Python 2.6. | |
| multiqc | 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. | Biological Sciences |
| mummer | 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. | Biological Sciences |
| mumps | 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. | Mathematics |
| musl | 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. | Computer & Information Sciences |
| mvapich-plus | MVAPICH-Plus is a high-performance implementation of the Message Passing Interface (MPI) standard, designed for high-performance computing (HPC) environments. It is optimized for various interconnects and provides advanced features for performance and scalability. | Computer Science |
| mvapich2-gdr | 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. | Engineering & Technology |
| mygene | MyGene is a Python package that provides a simple interface to access gene-related data from various public databases, including gene annotations, gene expression data, and more. | Genetics |
| namd | 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. | Biochemistry and Molecular Biology |
| namd-multicore-cuda | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | |
| namd-netlrts-smp-cuda | 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. | Biological Sciences |
| namd-verbs-smp-cuda | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. | |
| nano | Nano is a simple and user-friendly text editor for Unix-like systems, designed to be easy to use for beginners while still providing powerful features for advanced users. | Computer Science |
| nanobind | ||
| nanoget | Functions to extract information from Oxford Nanopore sequencing data and alignments. Data can be presented in the following formats, using the following functions: - A sorted bam file process_bam(bamfile, threads) - A standard fastq file process_fastq_plain(fastqfile, 'threads') - A fastq file with metadata from MinKNOW or Albacore process_fastq_rich(fastqfile) - A sequencing_summary file generated by Albacore process_summary(sequencing_summary.txt, 'readtype') | |
| nanomath | A few simple math functions for other Oxford Nanopore processing scripts: - Calculate read N50 from a set of lengths get_N50(readlenghts) - Remove extreme length outliers from a dataset remove_length_outliers(dataframe, columname) - Calculate the average Phred quality of a read ave_qual(qualscores) - Write out the statistics report after calling readstats function write_stats(dataframe, outputname) - Compute a number of statistics, return a dictionary calc_read_stats(dataframe) | |
| nasm | 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. | Computer & Information Sciences |
| nbclassic | nbclassic is a classic Jupyter Notebook interface that allows users to create and share documents that contain live code, equations, visualizations, and narrative text. | Data Science |
| ncbi-vdb | 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. | Biological Sciences |
| nccl | 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. | Computer & Information Sciences |
| ncl | 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. | Earth & Environmental Sciences |
| nco | 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. | Earth & Environmental Sciences |
| ncurses | ncurses is a programming library providing an API that allows the programmer to write text-based user interfaces on a terminal. | Computer & Information Sciences |
| neci | neci is a state-of-the-art implementation of the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) algorithm, a method based on a stochastic application of the Hamiltonian matrix on a sparse sampling of the wave function. The program utilizes a very powerful parallelization and scales efficiently to more than 24 000 central processing unit cores. | |
| nedit | A fast, compact Motif/X11 plain text editor, for most popular Unix systems. Features significant support for programmers including syntax highlighting, macro language, and streamlined keyboard navigation. Mature and stable. | |
| neper | Neper is a software tool for generating and manipulating 3D polycrystalline microstructures. It is particularly useful in materials science for simulating the mechanical behavior of materials at the microscale. | Materials Science |
| netcdf | 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. | Other Natural Sciences |
| netcdf-c++4 | 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++. | Other Natural Sciences |
| netcdf-fortran | 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. | Other Natural Sciences |
| netcdf4-python | 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. | Earth & Environmental Sciences |
| nettle | 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. | Computer & Information Sciences, Computer Science |
| networkx | 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. | Computer & Information Sciences |
| nextflow | Nextflow is a powerful workflow manager that enables the writing of parallel and scalable computational workflows using native, containerized, or cloud-enabled execution environments. | Biological Sciences |
| nf-core | 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. | Biological Sciences |
| nghttp2 | 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. | Computer & Information Sciences |
| nghttp3 | 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. | Computer & Information Sciences |
| ngtcp2 | ngtcp2 is a C library implementation of the QUIC protocol (IETF draft) for building QUIC servers and clients. | Computer & Information Sciences |
| nibabel | 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. | Biological Sciences |
| ninja | 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. | Engineering & Technology |
| nlohmann_json | nlohmann_json is a JSON library for modern C++. It provides a simple and efficient way to work with JSON data in C++ programs. | Computer & Information Sciences |
| nlopt | 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. | Mathematics |
| nltk | 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. | Computer & Information Sciences |
| nmad | 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. | Other Mathematics |
| nodejs | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. It enables developers to build scalable network applications using JavaScript on the server side. | Software Engineering |
| nspr | 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. | Computer & Information Sciences |
| nss | 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. | Computer & Information Sciences |
| nsync | 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. | Engineering & Technology |
| ntl | 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. | Mathematics |
| ntpoly | NTPoly is a high-performance software library designed for computing polynomial expansions of large sparse matrices, particularly density matrices in electronic structure calculations. It implements efficient and scalable algorithms for recursive polynomial expansions, enabling linear scaling computations in quantum chemistry and materials science. | Physical Chemistry |
| numactl | 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. | Engineering & Technology |
| numba | Numba is an open-source just-in-time (JIT) compiler that translates a subset of Python and NumPy code into fast machine code. | Computer & Information Sciences |
| numpy | 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. | Computer & Information Sciences, Mathematics |
| nvhpc | 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. | Computer & Information Sciences |
| nvidia-cutlass | ||
| nvshmem | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| nvtop | 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. | Computer & Information Sciences |
| ocaml | OCaml is a general-purpose programming language with an emphasis on expressiveness and safety, featuring a powerful type system and automatic memory management. | Software Engineering |
| onnx | 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. | Computer & Information Sciences |
| onnx-runtime | ONNX Runtime is a high-performance inference engine for deploying machine learning models in production. It supports models in the Open Neural Network Exchange (ONNX) format and is designed to optimize performance across various hardware platforms. | Artificial Intelligence and Intelligent Systems |
| opari2 | 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. | Computer & Information Sciences |
| openbabel | Open Babel is an open-source chemical toolbox designed to facilitate the interconversion of chemical file formats and the manipulation of chemical data. | Molecular Modeling |
| openblas | 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. | Computer & Information Sciences |
| opencv | 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 & Information Sciences |
| openexr | 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. | Engineering & Technology |
| openfoam | 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. | Physical Sciences |
| openfold | 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. | Biological Sciences |
| opengl | OpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. It is widely used in video games, CAD applications, and virtual reality. | Computer and Information Sciences |
| openimageio | OpenImageIO is a library for reading and writing images, and a bunch of related functionality, like dealing with image formats and color management. | Computer & Information Sciences |
| openjpeg | 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. | Computer & Information Sciences |
| openmc | OpenMC is a community-developed, open-source code for simulating the transport of neutrons and photons in a variety of materials. It is designed for high-performance computing applications and supports a wide range of geometries and materials. | Nuclear Engineering |
| openmm | 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. | Biological Sciences |
| openmpi | 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. | Computer & Information Sciences |
| openpgm | 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. | Computer & Information Sciences |
| openpyxl | openpyxl is a Python library for reading and writing Excel (xlsx) files. It allows for the manipulation of Excel spreadsheets, enabling users to create, modify, and extract data from Excel files programmatically. | Computer Science |
| openscenegraph | 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. | Engineering & Technology |
| openssl | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| opensubdiv | 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. | Computer & Information Sciences |
| opt-einsum | opt-einsum is a Python library for optimizing the computation of Einstein summation convention expressions, enabling efficient tensor contractions in high-performance computing applications. | Applied Computer Science |
| optax | Optax is a gradient processing and optimization library for JAX, designed to facilitate the implementation of various optimization algorithms and gradient transformations. | Machine Learning |
| optix | 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. | Computer & Information Sciences |
| optree | optree is a software tool designed for the optimization and analysis of decision trees, particularly in the context of machine learning and data mining. It provides functionalities to construct, prune, and evaluate decision trees efficiently, supporting various splitting criteria and optimization strategies. | Artificial Intelligence and Intelligent Systems |
| optuna | 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. | Computer & Information Sciences |
| orca | 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. | Chemical Sciences |
| osi | 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. | Computer & Information Sciences |
| ospray | OSPRay is an open-source, scalable, and portable ray tracing engine for high-performance, photorealistic visualization. It is designed to leverage modern CPU architectures and supports interactive rendering of large-scale scientific data and complex scenes. | Visualization and Human-Computer Systems |
| osu-micro-benchmarks | 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. | Engineering & Technology |
| otf2 | 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. | Engineering & Technology |
| p11-kit | 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. | Computer & Information Sciences |
| p7zip | 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. | Computer & Information Sciences |
| padicotm | 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. | Engineering & Technology |
| pandoc | Pandoc is a universal document converter that allows users to convert files from one markup format to another. It supports a wide range of formats including Markdown, HTML, LaTeX, and many others. | Computer and Information Sciences |
| pango | 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. | Computer & Information Sciences |
| papi | 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. | Computer Science |
| parabricks | 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. | Biological Sciences |
| parafold | 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. | Biological Sciences |
| parallel | 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. | Computer & Information Sciences |
| parameterized | parameterized is a Python library that simplifies the creation of parameterized unit tests, allowing developers to run the same test logic with different sets of input data easily and cleanly. | Software Engineering, Systems, and Development |
| paramiko | Paramiko is a Python library that provides an implementation of the SSHv2 protocol, enabling secure connections to remote machines for executing commands, transferring files, and managing SSH sessions programmatically. | Computer Science |
| paraview | 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. | Physical Sciences, Engineering & Technology, Natural Sciences, Computer & Information Sciences, Other Natural Sciences |
| paraview-catalyst | ParaView Catalyst is an in situ data analysis and visualization library that integrates with simulation codes to perform live data processing and visualization during simulation runtime, eliminating the need for large data storage and post-processing. | Visualization and Human-Computer Systems |
| parmetis | 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. | Computer & Information Sciences |
| parsl | Parsl is a parallel scripting library for Python that allows users to easily write parallel applications and workflows, enabling efficient execution of tasks across various computing resources. | Computer Science |
| pasa | PASA (Program to Assemble Spliced Alignments) is a software tool designed for the alignment and assembly of transcript sequences, particularly useful in the context of RNA-Seq data analysis. | Genomics |
| patchelf | PatchELF is a simple utility for modifying the dynamic linker and run-time library paths in executable files. | Computer & Information Sciences |
| patsy | Patsy is a Python library for describing statistical models and building design matrices using a formula syntax similar to R. It facilitates the specification of linear models and other statistical models by parsing symbolic formulas and generating matrices suitable for regression and other analyses. | Statistics and Probability |
| pblat | 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. | Biological Sciences |
| pcre | 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. | Computer & Information Sciences |
| pcre2 | 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. | Computer & Information Sciences |
| pdal | 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. | Other Natural Sciences |
| pdm | PDM (Python Development Master) is a package and dependency management tool for Python projects, designed to simplify the management of project dependencies and environments. | Software Engineering |
| pdt | 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. | Computer & Information Sciences |
| perl | 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. | Computer & Information Sciences |
| perl-bundle-cpan | A collection of Perl modules that can be installed using CPAN, providing a convenient way to manage Perl dependencies. | Software Engineering |
| perl-bundle1-cpan | A collection of Perl modules and libraries available on CPAN (Comprehensive Perl Archive Network) bundled together for easy installation and management. | Computer & Information Sciences |
| perl-bundle2-cpan | 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. | Computer & Information Sciences |
| petsc | 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. | Natural Sciences |
| petsc4py | petsc4py is a Python wrapper for the Portable, Extensible Toolkit for Scientific Computation (PETSc), which provides a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. | Numerical Methods |
| pfft | PFFT (Parallel FFT) is a parallel library for computing fast Fourier transforms (FFTs) on distributed-memory systems. It extends the FFTW library to support scalable multidimensional FFTs on large-scale parallel computers using MPI for communication. | Applied Mathematics |
| phylip | PHYLIP (Phylogeny Inference Package) is a software package for inferring phylogenies (evolutionary trees) from DNA or protein sequences. | Evolutionary Biology |
| physics-tenpy | 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/ | |
| picard | 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. | Biological Sciences |
| pigz | 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. | Computer & Information Sciences |
| pillow | Pillow is a powerful Python Imaging Library (PIL) replacement that adds image processing capabilities to your Python interpreter. | Computer & Information Sciences, Software Engineering, Systems & Development |
| pillow-simd | pillow-simd is an optimized fork of Python imaging library (PIL) with SIMD support, designed to enhance image processing capabilities with improved performance. | Computer & Information Sciences |
| pioman | 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. | Computer & Information Sciences |
| pipenv | Pipenv is a packaging tool for Python that aims to bring the best of all packaging worlds (bundled, required, and development dependencies) to the Python world. It manages dependencies, virtual environments, and simplifies the process of managing Python projects. | Software Engineering |
| pixi | Pixi is a fast, modern, and reproducible package management tool for developers of all backgrounds. | |
| pixman | 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. | Computer & Information Sciences |
| pkg-config | 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. | Engineering & Technology |
| pkgconf | 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. | Computer & Information Sciences |
| pkgconfig | 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. | Engineering & Technology |
| plink | 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. | Biological Sciences |
| plotly.py | 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. | Computer & Information Sciences |
| plumed | 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. | Biological Sciences |
| ply | 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. | Computer & Information Sciences |
| pmix | 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. | Engineering & Technology |
| pnetcdf | 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. | Physical Sciences |
| pocl | 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. | Computer & Information Sciences |
| poetry | 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. | Computer & Information Sciences |
| polars | Polars is a fast DataFrame library implemented in Rust and designed for performance and ease of use in data manipulation and analysis. | Software Engineering |
| poppler | 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. | Computer & Information Sciences |
| portmidi | PortMidi is a portable MIDI input/output library designed for use with C, C++, and other programming languages. It provides a simple interface for MIDI communication across various platforms. | Computer Science |
| postgresql | 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. | Computer Science |
| pov-ray | 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. | Computer Science |
| pplacer | 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. | Biological Sciences |
| prank | 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. | Biological Sciences |
| prodigal | 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. | Biological Sciences |
| proj | 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. | Other Natural Sciences |
| prokka | 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. | Biological Sciences |
| prompt-toolkit | prompt-toolkit is a Python library for building powerful interactive command line applications. It provides advanced input editing, syntax highlighting, autocompletion, multi-line editing, and other features to create rich user interfaces in terminal environments. | Software Engineering, Systems, and Development |
| protobuf | 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. | Computer & Information Sciences |
| protobuf-python | protobuf-python is a Python library for Protocol Buffers, Google's language-neutral, platform-neutral extensible mechanism for serializing structured data. | Computer & Information Sciences |
| prrte | 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. | Engineering & Technology |
| psutil | psutil is a cross-platform library for process and system monitoring in Python. It provides an interface for retrieving information on running processes and system utilization (CPU, memory, disks, network, sensors) in a portable way. | Other Computer and Information Sciences |
| psycopg2 | 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. | Computer & Information Sciences |
| ptex | A high-quality Japanese typesetting system based on TeX that is specifically optimized for the Japanese language. | Humanities |
| pugixml | 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. | Computer & Information Sciences |
| puk | PM2 is an umbrella software suite for high-performance runtime systems. Modules may be installed and used together or separately. | |
| pukabi | Pukabi is a bioinformatics tool used for analyzing and visualizing phylogenetic trees. | Biological Sciences |
| pulp | PuLP is a Python library for modeling linear programming problems. It allows users to describe optimization problems in a natural way and provides a simple interface to various solvers. | Mathematics |
| py-cpuinfo | 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. | Computer & Information Sciences |
| py3dmol | 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. | Chemical Sciences, Biological Sciences |
| pyberny | pyberny is a Python interface and implementation of the Berny optimization algorithm for geometry optimization of molecular structures. It is designed to perform energy minimizations and transition state searches using internal coordinates, commonly used in computational chemistry workflows. | Physical Chemistry |
| pybigwig | pyBigWig is a Python interface for working with BigWig files, a binary format for efficiently storing genome-wide signal data. | Biological Sciences |
| pybind11 | 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. | Computer & Information Sciences |
| pybind11-stubgen | ||
| pybiolib | pybiolib is a Python client library designed to interact with BioLib, a biological data resource. It facilitates programmatic access to biological datasets and services, enabling users to query, retrieve, and manipulate biological information efficiently within Python environments. | Biological Sciences |
| pycairo | 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. | Computer & Information Sciences |
| pychemps2 | pychemps2 is a Python package for performing multiconfigurational perturbation theory calculations, specifically implementing the second-order N-electron valence state perturbation theory (NEVPT2) method. It is designed to interface with quantum chemistry packages to provide accurate dynamic correlation corrections on top of multireference wavefunctions. | Physical Chemistry |
| pycuda | 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. | Computer & Information Sciences |
| pycurl | pycurl is a Python interface to the cURL library, allowing for easy HTTP requests and data transfer. | Software Engineering |
| pydantic | 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. | Computer & Information Sciences |
| pydicom | 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. | Medical & Health Sciences |
| pydot | Pydot is a Python interface for Graphviz's Dot language, allowing users to create, manipulate, and visualize graphs and networks. | Computer Science |
| pyem | pyem is a Python package designed for cryo-electron microscopy (cryo-EM) image processing. It provides tools for particle picking, image alignment, classification, and reconstruction to facilitate high-resolution 3D structure determination of macromolecules from cryo-EM data. | Biophysics |
| pyfaidx | 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. | Biological Sciences |
| pyfr | PyFR is an open-source Python-based framework for solving fluid dynamics problems on many-core architectures. | Physical Sciences |
| pygame | Pygame is a set of Python modules designed for writing video games. It provides functionalities like creating windows, drawing shapes, handling images, sounds, and events, making it easier to develop games and multimedia applications. | Computer Science |
| pygments | ||
| pygobject | 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. | Computer & Information Sciences |
| pyopengl | 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. | Computer & Information Sciences |
| pyopenssl | pyOpenSSL is a Python library that provides a high-level interface to the OpenSSL cryptographic library, enabling the use of SSL/TLS protocols and cryptographic functions in Python applications. | Computer Science |
| pyproj | Pyproj is a Python interface to the PROJ library for cartographic projections and coordinate transformations. | Earth & Environmental Sciences |
| pyqt-builder | pyqt-builder is a Python package that provides tools to facilitate building and packaging PyQt applications. It integrates with setuptools to automate the compilation of Qt Designer .ui files, resource files, and translation files into Python modules, streamlining the application build process. | Software Engineering, Systems, and Development |
| pyqt5 | 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. | Computer & Information Sciences |
| pyrosetta | PyRosetta is a Python-based interface to the Rosetta molecular modeling suite, which is widely used for protein structure prediction and design. | Molecular Modeling |
| pysam | 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. | Biological Sciences |
| pyscf | PySCF (Python-based Simulations of Chemistry Framework) is an open-source computational chemistry software package designed for electronic structure calculations. It provides a flexible and efficient platform for quantum chemistry simulations, supporting a wide range of methods including Hartree-Fock, density functional theory, post-Hartree-Fock methods, and periodic boundary conditions. | Physical Chemistry |
| pytensor | 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. | Computer & Information Sciences |
| pytesseract | Pytesseract is a Python wrapper for Google's Tesseract-OCR Engine. It allows for easy integration of Tesseract OCR functionality in Python scripts. | Computer & Information Sciences |
| pytest | 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. | Computer & Information Sciences |
| pytest-flakefinder | 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. | Engineering & Technology |
| pytest-rerunfailures | pytest-rerunfailures is a plugin for the pytest testing framework that automatically reruns failed test cases to improve test reliability. | Engineering & Technology |
| pytest-shard | 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. | Computer & Information Sciences |
| pytest-subtests | ||
| pytest-workflow | pytest-workflow is a Python testing framework extension designed to facilitate the testing of complex workflows and pipelines. It provides utilities and decorators to manage multi-step workflows, enabling users to define, run, and validate sequences of dependent tasks within pytest tests. | Software Engineering, Systems, and Development |
| pytest-xdist | 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. | Computer & Information Sciences |
| pythia | 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. | Physical Sciences |
| python | 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. | Computer & Information Sciences, Software Engineering, Systems & Development |
| python-bundle-pypi | 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. | Computer & Information Sciences |
| python-isal | Python bindings for Intel Storage Acceleration Library (ISAL) that provides optimized functions for storage protocols and data transformation. | Computer & Information Sciences |
| python-xxhash | A Python wrapper for the xxHash algorithm, which is known for its high speed and good distribution properties. | Other Computer and Information Sciences |
| python-zlib-ng | python-zlib-ng is a Python binding for zlib-ng, a modern replacement for the widely used zlib compression library. It provides fast, efficient compression and decompression capabilities with improved performance and additional features compared to the original zlib. | Software Engineering |
| pytorch | PyTorch is an open-source machine learning library used for numerical computations and building deep learning models. | Computer & Information Sciences |
| pytorch-bundle | pytorch-bundle is a curated and pre-packaged distribution of the PyTorch deep learning framework and its commonly used dependencies, designed to simplify deployment and usage in high-performance computing (HPC) environments. It provides a ready-to-use, consistent PyTorch environment that includes optimized libraries for GPU acceleration, distributed training, and popular extensions. | Artificial Intelligence and Intelligent Systems |
| pytorch-geometric | PyTorch Geometric is a library for deep learning on irregular structures such as graphs, point clouds, and manifolds. It provides a set of tools to easily implement graph neural networks and other related models. | Artificial Intelligence and Intelligent Systems |
| pytorch-lightning | PyTorch Lightning is a lightweight wrapper around PyTorch that helps to organize PyTorch code and decouple the science code from the engineering code, making it easier to scale and maintain. | Deep Learning |
| pyyaml | 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. | Computer & Information Sciences |
| pyzmq | 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. | Computer & Information Sciences |
| pyzstd | pyzstd is a Python binding for the Zstandard (zstd) compression library, enabling fast and efficient compression and decompression of data using the Zstandard algorithm directly from Python applications. | Software Engineering, and Development |
| qca | 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. | Social Sciences |
| qcint | qcint is a computational chemistry software package specialized in the calculation of molecular integrals over Gaussian basis functions. It provides efficient and accurate evaluation of one- and two-electron integrals essential for quantum chemistry methods such as Hartree-Fock and post-Hartree-Fock calculations. | Physical Chemistry |
| qemu | 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. | Computer & Information Sciences |
| qgis | QGIS is a free and open-source cross-platform desktop geographic information system (GIS) application that supports viewing, editing, and analysis of geospatial data. | Earth & Environmental Sciences |
| qhull | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. | Other Mathematics |
| qiime2 | QIIME 2 is an open-source bioinformatics platform for performing microbiome analysis. It provides a comprehensive suite of tools for analyzing and visualizing microbial communities from amplicon sequencing data. | Bioinformatics |
| qiskit | Qiskit is an open-source quantum computing software development framework that provides tools for creating, simulating, and executing quantum programs. | Quantum Algorithms |
| qjson | QJson is a Qt-based library that maps JSON data to QVariant objects. It allows for easy JSON serialization and deserialization in Qt applications. | Computer & Information Sciences |
| qmsolve | qmsolve is a Python package designed for solving quantum master equations, particularly for open quantum systems. It provides tools to model and simulate the dynamics of quantum systems interacting with environments, using various master equation formalisms such as the Lindblad equation. | Atomic, Molecular, and Optical Physics |
| qorts | QoRTs (Quality of RNA-Seq Toolset) is a comprehensive software package designed for quality control and data processing of RNA-Seq datasets. It provides detailed metrics and visualizations to assess RNA-Seq data quality and supports downstream analyses such as gene expression quantification and junction analysis. | Biological Sciences |
| qscintilla | 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. | Engineering & Technology |
| qt5 | 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. | Engineering & Technology |
| qt5webkit | 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. | Computer & Information Sciences |
| qt6 | Qt 6 is a cross-platform application framework that is widely used for developing application software with a graphical user interface (GUI) as well as non-GUI programs such as command-line tools and consoles for servers. | Software Engineering |
| qtkeychain | QtKeychain is a Qt API to store passwords securely | Software Engineering |
| qualimap | 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. | Biological Sciences |
| quantum machine 9 (qm9) | Quantum Machine 9 (QM9) dataset for quantum chemistry and machine learning, containing detailed quantum chemical calculations for a large set of small organic molecules | |
| quantumespresso | Quantum ESPRESSO is an integrated suite of computer codes for electronic structure calculations and materials modeling at the nanoscale. | Condensed Matter Physics |
| quast | 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. | Biological Sciences |
| quda | QUDA (Quda) is a library for solving quantum chromodynamics (QCD) problems on GPUs, providing high-performance implementations of lattice QCD algorithms. | Quantum Chromodynamics |
| qwt | 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. | Engineering & Technology |
| r | 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. | Computer Science |
| r-bundle-bioconductor | Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. | Biological Sciences |
| r-bundle-cran | A collection of R packages that are available on CRAN (Comprehensive R Archive Network) for various statistical and graphical techniques. | Statistical Computing |
| r_tamu | r_tamu is a simulation software for thermal and mechanical unit operations in chemical engineering. | Engineering & Technology |
| racon | 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. | Biological Sciences |
| raja | RAJA is a performance portability library developed by Lawrence Livermore National Laboratory that enables developers to write portable parallel code for HPC applications. It abstracts parallel loop execution and memory access patterns, allowing the same source code to run efficiently on different hardware backends such as CPUs, GPUs, and many-core architectures. | Computer Science |
| rapidjson | 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. | Computer & Information Sciences |
| rapids | 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. | Computer & Information Sciences |
| rapsearch2 | RapSearch2 is a high-performance sequence alignment tool designed for rapid and sensitive alignment of protein sequences against large databases. | Bioinformatics |
| rastair | rastair is a Rust-based software tool designed for methylation analysis in bisulfite sequencing data workflows. It is used as part of pipelines such as nf-core/methylseq to perform methylation calling and analysis, complementing aligners like bwa-mem. | |
| rasterio | 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. | Earth & Environmental Sciences |
| rattler-build | rattler-build is a command-line tool designed to create and manage software environments and packages for scientific computing and data science workflows. It is part of the rattler ecosystem, which provides environment management and package building capabilities similar to conda, focusing on reproducibility and cross-platform compatibility. | Software Engineering, Systems, and Development |
| raven | Raven is a de novo genome assembler for long uncorrected reads. | |
| ray-project | Ray is a flexible, high-performance distributed execution framework that makes it easy to scale Python applications from a single machine to a cluster. | Artificial Intelligence and Intelligent Systems |
| rclone | 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. | Computer Science |
| rdflib | 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. | Computer & Information Sciences |
| rdkit | 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. | Natural Sciences |
| re2 | 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. | Computer & Information Sciences |
| re2c | 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. | Computer & Information Sciences |
| redis | 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. | Computer & Information Sciences |
| redis-py | 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. | Computer & Information Sciences |
| reframe | 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. | Engineering & Technology |
| relion | 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). | Biochemistry and Molecular Biology |
| requests | Requests is a simple and elegant HTTP library for Python, built for human beings. | Other Computer and Information Sciences |
| rich | Rich is a Python library for rich text and beautiful formatting in the terminal. | Computer & Information Sciences |
| rioxarray | 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. | Earth & Environmental Sciences |
| rising | 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. | Engineering & Technology |
| rnaquast | 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. | Biological Sciences |
| robin-map | ||
| rocm-smi | 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. | Engineering & Technology |
| root | 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. | Physical Sciences |
| rosetta | Rosetta is a software suite for modeling macromolecules, including protein folding, protein-protein interactions, and protein-ligand docking. It provides tools for predicting and designing protein structures, protein-protein interactions, and protein-ligand binding. | Structural Biology |
| rpds-py | ||
| rpmrebuild | A tool for rebuilding RPM packages from existing RPM files. | Software Engineering |
| rsem | 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. | Biological Sciences |
| rseqc | RSeQC provides a number of standalone modules to check quality of RNA-Seq experiments, from raw data to the final result. | Biological Sciences |
| ruamel.yaml | 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). | Computer & Information Sciences |
| ruby | 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. | Computer Science |
| rust | Rust is a multi-paradigm system programming language focused on safety, speed, and concurrency. | Computer & Information Sciences |
| safestringlib | A library for safe string handling in C/C++ to prevent buffer overflows and other vulnerabilities. | Software Engineering |
| safetensors | Safe and fast tensor serialization format and library for machine-learning model weights. It can be loaded as a software module on the listed HPC resource and used in batch or interactive workflows. | |
| salmon | Salmon is a wicked-fast program to provide quantification of transcript expression from RNA-seq data. | Biological Sciences |
| samtools | 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. | Biological Sciences |
| scafacos | 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. | Biological Sciences |
| scalapack | 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. | Physical Sciences |
| scalasca | 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. | Computer & Information Sciences |
| scalene | Scalene is a high-performance, high-precision CPU, GPU, and memory profiler for Python. It provides detailed insights into the performance of Python code, allowing developers to identify bottlenecks and optimize their applications effectively. | Software Engineering |
| schrodinger | 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. | Chemical Sciences |
| scikit-bio | 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. | Biological Sciences |
| scikit-build | 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. | Computer & Information Sciences |
| scikit-build-core | scikit-build-core is a core library for building Python packages with CMake, designed to simplify the process of creating Python extensions and modules. | Software Engineering |
| scikit-cuda | 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. | Computer & Information Sciences |
| scikit-image | 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. | Computer & Information Sciences |
| scikit-learn | 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. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| scipy-bundle | 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. | Computer & Information Sciences, Other Computer & Information Sciences |
| scons | 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. | Engineering & Technology |
| score-p | 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. | Engineering & Technology |
| scotch | 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. | Computer & Information Sciences |
| sdl2 | 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. | Engineering & Technology |
| sdl2_image | SDL2_image is an image loading library that is part of the Simple DirectMedia Layer (SDL) project. It allows developers to load various image formats into SDL surfaces and textures, making it easier to work with images in multimedia applications and games. | Computer Science |
| sdl2_mixer | SDL2_mixer is a simple multi-channel audio mixer library for use with SDL2. It provides support for various audio formats and allows for easy mixing of multiple audio sources. | Software Engineering |
| sdl2_ttf | SDL2_ttf is a library that provides TrueType font support for the Simple DirectMedia Layer (SDL) library. It allows developers to render text using TrueType fonts in their SDL applications. | Other Computer and Information Sciences |
| sdsl-lite | SDSL-lite is a lightweight C++ library for the implementation of succinct data structures, which are space-efficient representations of data that allow for fast access and modification. | Computer Science |
| seaborn | Seaborn is a Python data visualization library based on matplotlib. It provides a high-level interface for creating attractive and informative statistical graphics. | Computer & Information Sciences |
| sentencepiece | 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. | Computer & Information Sciences |
| sepp | 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. | Biological Sciences |
| seqkit | 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. | Biological Sciences |
| seqlib | C++ interface to HTSlib, BWA-MEM and Fermi. | |
| seqtk | Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It is designed for handling large sequence data efficiently. | Biological Sciences |
| serf | 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. | Engineering & Technology |
| settarg | 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. | |
| setuptools | 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. | Computer Science |
| setuptools-rust | 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. | Computer & Information Sciences |
| shap | 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. | Computer & Information Sciences |
| shapely | 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. | Earth & Environmental Sciences |
| siesta | 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. | Physical Sciences |
| simple-dftd3 | Lightweight implementation of Grimme DFT-D3 dispersion corrections for atomistic simulations. | |
| sionlib | 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. | Computer Science |
| sip | SIP (Session Initiation Protocol) is a protocol used for initiating, maintaining, and terminating real-time sessions that include voice, video, and messaging applications. | Computer Science |
| skani | ||
| slepc | SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems. | Other Mathematics |
| smithwaterman | Smith-Waterman is an algorithm used for local sequence alignment in bioinformatics, particularly for comparing protein or nucleotide sequences. | Bioinformatics |
| smv | Smokeview is a visualization program that displays output of FDS and CFAST simulations. | |
| snakemake | 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. | Other Computer & Information Sciences |
| snappy | 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. | Computer & Information Sciences |
| sox | SoX (Sound eXchange) is a command-line utility that converts various formats of computer audio files in to other formats. It can also apply various effects to the audio. | Audio Engineering |
| spack | 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. | Other Computer & Information Sciences |
| spacy | 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. | Computer & Information Sciences |
| spades | 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. | Biological Sciences |
| spark | Apache Spark is an open-source distributed computing system that provides an interface for programming entire clusters with implicit data parallelism and fault tolerance. | Computer & Information Sciences |
| sparsehash | 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. | Computer & Information Sciences |
| spfft | Sparse three-dimensional FFT library designed for distributed-memory electronic-structure applications. It can be loaded as a software module on the listed HPC resource and used in batch or interactive workflows. | |
| spglib | 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. | Physical Sciences |
| spglib-python | 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. | Physical Sciences |
| spin | Spin provides a simple, user-friendly, extendable interface for common development tasks. It comes with a few common build commands out the box, but can easily be customized per project. | |
| spython | 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. | Computer & Information Sciences, Other Mathematics, Other Natural Sciences |
| sqlalchemy | SQLAlchemy is a SQL toolkit and Object-Relational Mapping (ORM) system for the Python programming language. | Database Systems |
| sqlite | 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. | Computer & Information Sciences |
| sra-toolkit | The SRA Toolkit is a collection of tools for working with data from the Sequence Read Archive (SRA). It allows users to download, convert, and manipulate sequencing data. | Genomics |
| sst-core | SST (Structural Simulation Toolkit) Core is a framework for developing high-performance simulations of complex systems, particularly in the field of computer architecture and systems. | Computer Science |
| ssw | SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. | |
| star | 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. | Biological Sciences |
| starpu | 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. | Other |
| statsmodels | 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 & Probability |
| strace | 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. | Computer & Information Sciences |
| stringtie | 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. | Biological Sciences |
| subread | 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. | Biological Sciences |
| subversion | 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. | Computer Science |
| suitesparse | 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. | Other Mathematics |
| sundials | 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. | Other Mathematics |
| superlu | 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. | Mathematics |
| superlu_dist | 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. | Mathematics |
| svt-av1 | SVT-AV1 is a high-performance AV1 video encoder developed by Intel's SVT (Scalable Video Technology) team. It aims to provide a scalable and efficient encoding solution for AV1 video compression. | |
| swig | 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. | Computer & Information Sciences, Software Engineering, Systems & Development |
| syclomatic | Intel migration tool that converts CUDA source code to SYCL for cross-architecture accelerator programming. | |
| sympy | 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. | Mathematics |
| synthcity | 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. | |
| szip | 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. | Computer Science |
| tabixpp | C++ wrapper around HTSlib tabix indexing and querying functionality. | |
| talloc | talloc is a hierarchical, reference counted memory pool system designed for C and C++ programming. It allows for easy memory management and helps prevent memory leaks. | Other Computer and Information Sciences |
| tbb | 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. | Computer & Information Sciences |
| tbl2asn | tbl2asn is a software tool used for converting tab-delimited files into ASN.1 format for submission to GenBank and other databases. | Genomics |
| tblis | tblis is a tensor contraction library designed for high-performance computing, focusing on efficient tensor operations and contractions, particularly in the context of scientific computing and numerical simulations. | |
| tcl | 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. | Computer & Information Sciences |
| tcsh | 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. | Computer & Information Sciences |
| tensorboard | 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. | Computer & Information Sciences |
| tensorboardx | 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. | Computer & Information Sciences |
| tensorflow | TensorFlow is an open-source machine learning library developed by Google to build and train deep learning models. | Computer & Information Sciences |
| tensorflow-probability | TensorFlow Probability is a library for probabilistic reasoning and statistical analysis in TensorFlow. It provides tools for building probabilistic models, performing Bayesian inference, and working with probabilistic distributions. | Artificial Intelligence and Intelligent Systems |
| tensorrt | 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. | Computer & Information Sciences |
| tensorstore | TensorStore is a library for managing multi-dimensional arrays and tensors with support for various storage backends, including in-memory, disk, and cloud storage. | Other Computer and Information Sciences |
| tesseract | 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. | Computer & Information Sciences |
| test-drive | This project offers a lightweight, procedural unit testing framework based on nothing but standard Fortran. | |
| texlive | TeX Live is a comprehensive distribution of TeX and related programs, providing a complete environment for typesetting documents. | Computer Science |
| theano | 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. | Computer & Information Sciences |
| tibs | tibs is a sleek Python library designed for efficient manipulation and parsing of binary data. It provides utilities to read, write, and transform binary streams with a clean and Pythonic API. | Software Engineering, and Development |
| time | 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. | Other |
| tk | 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. | Computer & Information Sciences, Computer Science, Software Engineering, Systems & Development |
| tkinter | 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. | Computer & Information Sciences |
| tlparse | Parse structured PT2 (PyTorch 2) logs | |
| tmux | 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. | Computer & Information Sciences |
| tokenizers | Tokenizers is a library for training and using tokenizers in natural language processing tasks. It provides a fast and efficient way to preprocess text data for machine learning models. | Natural Language Processing |
| toml-fortran | TOML parser and serializer implemented for modern Fortran. It can be loaded as a software module on the listed HPC resource and used in batch or interactive workflows. | |
| topaz | Particle picking software for single particle cryo-electron microscopy using convolutional neural networks and positive-unlabeled learning. Includes methods for micrograph denoising. | |
| torchsampler | 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. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| torchtext | 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. | Computer & Information Sciences |
| torchvision | 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. | Computer & Information Sciences |
| tornado | 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. | Computer & Information Sciences |
| tqdm | 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. | Computer & Information Sciences |
| transdecoder | 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. | Biological Sciences |
| transformers | 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. | Computer & Information Sciences |
| transrate | 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. | Biological Sciences |
| trilinos | 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. | Engineering & Technology |
| trim_galore | Trim Galore! is a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. | Biochemistry and Molecular Biology |
| trimmomatic | 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. | Biological Sciences |
| trinity | 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. | Biological Sciences |
| trinotate | 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. | Biological Sciences |
| triton | Triton is a programming language and compiler designed to facilitate the development of high-performance deep learning applications on GPUs. | Computer Science |
| turm | turm is a terminal user interface (TUI) designed to interact with and manage jobs on the Slurm Workload Manager. It provides a user-friendly, interactive command-line interface to view, submit, and control Slurm jobs efficiently. | Computer Science |
| twisted | 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. | Computer & Information Sciences |
| typing-extensions | 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. | Computer & Information Sciences |
| ucc | 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. | Natural Sciences |
| ucc-cuda | 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. | Computer & Information Sciences, Engineering & Technology |
| ucx | Unified Communication X (UCX) is a flexible and high-performance communication library for applications and libraries. | Computer Science |
| ucx-cuda | 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. | Computer & Information Sciences |
| udunits | 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. | Computer and Information Sciences |
| umap-learn | UMAP (Uniform Manifold Approximation and Projection) is a dimensionality reduction technique that is particularly well-suited for visualizing high-dimensional data. | Artificial Intelligence and Intelligent Systems |
| umoci | umoci is a tool for managing Open Container Initiative (OCI) images. It allows users to create, modify, and unpack OCI container images. | Software Engineering |
| uni-core | An efficient distributed PyTorch framework | |
| unicycler | 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. | Biological Sciences |
| unifrac | UniFrac is a bioinformatics tool used to compare the phylogenetic diversity of microbial communities based on their DNA sequences. | Ecology |
| unittest-xml-reporting | A unittest test runner that can save test results to XML files in xUnit format. The files can be consumed by a wide range of tools, such as build systems, IDEs and continuous integration servers. | |
| unzip | 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. | Computer & Information Sciences |
| utf8proc | 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. | Computer & Information Sciences |
| util-linux | 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. | Computer & Information Sciences |
| uv | uv is a high-performance Python package manager, project manager, and virtual environment tool designed as a fast, drop-in replacement for pip, pipx, venv, and virtualenv. | |
| valgrind | Valgrind is a programming tool for memory debugging, memory leak detection, and profiling. It can also be used for cache and thread error detection. | Computer & Information Sciences |
| vasp | 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. | Physical Sciences, Engineering & Technology |
| vcflib | vcflib is a C++ library for parsing and manipulating Variant Call Format (VCF) files, which are commonly used in bioinformatics for storing gene sequence variations. | Genomics |
| vcftools | 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. | Biological Sciences |
| velvet | 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. | Biological Sciences |
| versioningit | Python tool that derives package versions from version-control metadata during builds. | |
| vesta | 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. | Chemical Sciences |
| virtualenv | 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. | Computer & Information Sciences |
| virtualgl | 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. | Computer & Information Sciences |
| visit | 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. | Computer & Information Sciences |
| vmd | 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. | Biological Sciences |
| voro++ | 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. | Mathematics |
| vscode | Visual Studio Code (VSCode) is a source-code editor developed by Microsoft that includes support for debugging, syntax highlighting, intelligent code completion, snippets, code refactoring, and embedded Git. | Computer Science |
| vsearch | 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. | Biological Sciences |
| vtk | 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. | Physical Sciences |
| vtune | 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. | Computer & Information Sciences |
| vulkan | Vulkan is a low-overhead, cross-platform 3D graphics and computing API that provides high-efficiency access to modern GPUs. | |
| vulkansdk | The Vulkan SDK provides a comprehensive set of tools, libraries, and documentation for developers to create high-performance graphics applications using the Vulkan API. | Computer Science |
| wandb | Weights & Biases (wandb) is a tool for tracking machine learning experiments, visualizing results, and collaborating on projects. | Artificial Intelligence and Intelligent Systems |
| watchfiles | A simple but powerful Python library for creating, interpreting and manipulating binary data. | |
| wayland | 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. | Computer & Information Sciences |
| waylandpp | waylandpp is a C++ binding library for Wayland, which is a protocol for a compositor to talk to its clients. | Computer & Information Sciences |
| webkitgtk+ | 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+. | Computer & Information Sciences |
| webproxy | 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. | Computer & Information Sciences |
| weka | Weka is a collection of machine learning algorithms for data mining tasks. It contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. | Artificial Intelligence and Intelligent Systems |
| wfa2 | High-performance implementation of the wavefront alignment algorithm for pairwise sequence alignment. | |
| wget | 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. | Computer & Information Sciences |
| wpebackend-fdo | wpebackend-fdo is a software project that provides a backend implementation for WebKit's WPE WebKit using a Flatpak distributed runtime for sandboxing. | Computer & Information Sciences |
| wps | 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. | Other |
| wrapt | wrapt is a Python module for decorators, wrappers, and monkey patching. It provides a way to create decorators that can be applied to functions and methods, allowing for enhanced functionality and behavior. | Other Computer and Information Sciences |
| wrf | 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. | Earth & Environmental Sciences |
| wxpython | 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. | Computer & Information Sciences |
| wxwidgets | 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. | Engineering & Technology |
| x11 | 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. | Computer & Information Sciences |
| x264 | 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. | Engineering & Technology |
| x265 | 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. | Computer & Information Sciences |
| xarray | 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. | Other Natural Sciences |
| xcfun | Exchange-correlation functional library for density-functional theory calculations. It can be loaded as a software module on the listed HPC resource and used in batch or interactive workflows. | |
| xclip | xclip is a command-line utility that provides an interface to X selections (the clipboard) in X11 environments. | Other Computer and Information Sciences |
| xerces-c++ | 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. | Computer & Information Sciences |
| xgboost | XGBoost is an open-source software library which provides a gradient boosting framework for efficient and high-performance machine learning. | Computer & Information Sciences, Artificial Intelligence & Intelligent Systems |
| xlsxwriter | XlsxWriter is a Python module for creating Excel XLSX files. It allows for the generation of complex Excel files with features such as formatting, charts, and formulas. | Applied Computer Science |
| xml-libxml | 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. | Computer & Information Sciences |
| xmlf90 | xmlf90 is a native Fortran XML processing library that provides tools for parsing and generating XML documents. It includes event-driven SAX parsing, stream-based XPath-style searches, DOM parsing through FDOM, and XML generation through WXML. It is designed for scientific applications that need to process large XML files efficiently with a small memory footprint. | |
| xmltodict | xmltodict is a Python library that makes working with XML data as easy as working with JSON. It provides a simple way to convert XML to Python dictionaries and vice versa. | Applied Computer Science |
| xorg-macros | 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. | Computer & Information Sciences |
| xpmem | XPMEM is a kernel module that provides a kernel-level interface for sharing memory between processes. | Computer & Information Sciences |
| xprop | 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. | Computer & Information Sciences |
| xproto | X Window System protocol development files. | Computer & Information Sciences |
| xtb | xtb (eXtended Tight Binding) is a quantum chemistry software package designed for efficient calculations of molecular properties and simulations, particularly for large molecular systems. | Chemical Sciences |
| xvfb | Xvfb (X virtual framebuffer) is an in-memory display server for Unix-like systems that enable running graphical applications without a display. | Computer & Information Sciences |
| xxd | xxd is a command-line utility on Unix and Unix-like systems for creating a hex dump of a given file or standard input. | Other Computer & Information Sciences |
| xxhash | xxHash is an extremely fast non-cryptographic hash algorithm, providing high-speed hashing for data integrity checks. | Other Computer and Information Sciences |
| xz | 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. | Computer & Information Sciences |
| yacs | 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. | Computer & Information Sciences |
| yasm | 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. | Engineering & Technology |
| yaxt | 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. | Computer & Information Sciences |
| yell | Yell is an extensible logging library for Ruby applications. It provides configurable loggers, multiple output adapters, custom message formatting, severity levels, and support for sending log messages to destinations such as the console, files, and system logging services. | |
| z3 | 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. | Computer & Information Sciences |
| zarr | 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. | Computer & Information Sciences |
| zeromq | 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. | Computer & Information Sciences |
| zfp | 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. | Computer & Information Sciences |
| zip | 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. | Other Computer & Information Sciences |
| zlib | 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. | Computer & Information Sciences |
| zlib-ng | zlib-ng is a fast, efficient, and portable data compression library that is a drop-in replacement for zlib. It is designed to be compatible with zlib while providing improved performance and additional features. | Software Engineering |
| zoltan | 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. | Engineering & Technology |
| zstd | 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. | Computer & Information Sciences |
No software matches that name.
Storage Documentation
File System
| Directory | Path | Quota | Purge | Backup | Notes |
|---|---|---|---|---|---|
| Home | /home/<userid> | 10 GB, 10,000 files | Backed up daily | Small scripts, config files, not for general use | |
| Scratch | /scratch/user/<userid> | 1 TB, 250,000 files | Not backed up | Primary working directory for jobs, not for long-term storage. Data is also removed when quotas are exceeded. | |
| Project | /scratch/group/<projectid> | 5 TB, 500,000 files | Purged 90 days after allocation expires | Not backed up | Shared storage for group members |