Helios CPU
Some software in the list below may require an additional licence and may not be generally available to all PLGrid users.
ABAQUS
Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA.
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2024 |
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2025 |
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ABySS
Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
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2.3.7 |
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ACTC
ACTC converts independent triangles into triangle strips or fans.
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1.1 |
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AIMAll
AIMAll is an easy to use, accurate, reliable and efficient quantum chemistry software package for performing comprehensive, quantitative and visual QTAIM analyses of molecular systems - starting from molecular wavefunction data.
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19.02.13-linux_64bit |
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AMS
ADF Quantum Chemistry Package with GPGPU support (AMS)
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2023.104 |
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2024.102 |
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2024.106 |
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2025.101 |
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ANSYS
Ansys/Fluent
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2024R1 |
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2024R1.lua |
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2025R2 |
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AOCC
AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0
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4.2.0 |
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5.0.0 |
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AOCL
AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs.
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5.1.0 |
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AOCL-BLAS
AOCL-BLAS is AMD's optimized version of BLAS targeted for AMD EPYC and Ryzen CPUs.
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5.0 |
|
APBS
APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.
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3.0.0 |
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AQUA-DUCT
AQUA-DUCT is perfectly capable of tracing molecules that enter defined region of the macromolecule during MD simulation.
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1.0.11 |
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ASE
ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations in C of functions in ASE. ASE uses it automatically when installed.
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3.25.0 |
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ATK
ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
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2.38.0 |
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AUGUSTUS
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
Versions | Environment loading command (via Lmod) |
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3.5.0 |
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Amber
Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.
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22.5-AmberTools-23.6 |
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24.3-AmberTools-24.8 |
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24.3-AmberTools-25.0 |
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Armadillo
Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.
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12.8.0 |
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12.8.0 |
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AutoDock
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
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4.2.6 |
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AutoGrid
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
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4.2.6 |
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Autoconf
Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
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2.71 |
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2.72 |
|
2.71 |
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Automake
Automake: GNU Standards-compliant Makefile generator
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1.16.5 |
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1.16.5 |
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1.16.5 |
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Autotools
This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
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20220317 |
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20231222 |
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20220317 |
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BBMap
BBMap short read aligner, and other bioinformatic tools.
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39.01 |
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BCFtools
Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
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1.19 |
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BEEF
BEEF is a library-based implementation of the Bayesian Error Estimation Functional, suitable for linking against by Fortran- or C-based DFT codes. A description of BEEF can be found at http://dx.doi.org/10.1103/PhysRevB.85.235149.
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0.1.3 |
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0.1.3 |
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0.1.3 |
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0.1.3 |
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BLAST+
Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
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2.14.1 |
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BLAT
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
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3.7 |
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BLIS
BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries.
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0.9.0 |
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1.0 |
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BUSCO
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
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5.7.1 |
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BamTools
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
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2.5.2 |
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BeautifulSoup
Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping.
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4.12.2 |
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Biopython
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
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1.84 |
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1.84 |
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1.81 |
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Bison
Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
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3.8.2 |
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3.8.2 |
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3.8.2 |
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Blitz++
Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface
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1.0.2 |
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Boost
Boost provides free peer-reviewed portable C++ source libraries.
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1.83.0 |
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1.85.0 |
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1.83.0 |
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1.83.0 |
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Boost.MPI
Boost provides free peer-reviewed portable C++ source libraries.
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1.83.0-threadsafe |
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Boost.Python
Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
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1.83.0 |
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Bowtie
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
Versions | Environment loading command (via Lmod) |
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1.3.1 |
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Bowtie2
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
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2.5.1 |
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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 modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression. The specification of the Brotli Compressed Data Format is defined in RFC 7932.
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1.1.0 |
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CASTEP
CASTEP is an electronic structure materials modelling code based on density functional theory (DFT), with functionality including geometry optimization molecular dynamics, phonons, NMR chemical shifts and much more.
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22.11 |
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24.1 |
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25.1.2 |
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25.1.2 |
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CFITSIO
CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
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4.3.1 |
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CFOUR
CFOUR (Coupled-Cluster techniques for Computational Chemistry) is a program package for performing high-level quantum chemical calculations on atoms and molecules.
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2.1-omp |
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CGAL
The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library.
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5.6.1 |
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CLHEP
The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package.
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2.4.6.2 |
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2.4.6.4 |
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CMake
CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
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3.27.6 |
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3.29.3 |
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3.29.3 |
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3.26.5 |
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3.29.3 |
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CP2K
CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials.
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2023.1 |
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2024.1 |
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2025.1-libcp2k |
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2025.1 |
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2024.2 |
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2024.3 |
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2025.1 |
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CREST
CREST is an utility/driver program for the xtb program. Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.
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3.0.2 |
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CRYSTAL23
CRYSTAL is a general-purpose program for the study of crystalline solids, and the first which has been distributed publicly.
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1.0.1 |
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CUDA
CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
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12.4.0 |
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Catch2
A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later
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2.13.9 |
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2.13.10 |
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Cereal
cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone.
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1.3.2 |
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CheMPS2
CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry.
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1.8.12 |
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CoordgenLibs
Schrodinger-developed 2D Coordinate Generation
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3.0.2 |
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CppUnit
CppUnit is the C++ port of the famous JUnit framework for unit testing.
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1.15.1 |
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CrayCCE
Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: December 2023).
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23.12 |
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Cython
Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex).
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3.0.10 |
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DB
Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
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18.1.40 |
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DBCSR
DBCSR stands for Distributed Blocked Compressed Sparse Row. DBCSR is a library designed to efficiently perform sparse matrix-matrix multiplication, among other operations.
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2.5.0 |
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DB_File
Perl5 access to Berkeley DB version 1.x.
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1.859 |
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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; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed.
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1.15.8 |
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DFTB+
DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed.
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24.1 |
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DIRAC
DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
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24.0 |
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25.0 |
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24.0-int64 |
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25.0-int64 |
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Dalton
The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, https://www.daltonprogram.org/www/citation.html.
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2020.1-SMP |
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2020.1-maxorb-cc-1500 |
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DendroPy
A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
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4.5.2 |
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Doxygen
Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
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1.9.8 |
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ELPA
Eigenvalue SoLvers for Petaflop-Applications.
Versions | Environment loading command (via Lmod) |
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2019.11.001 |
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2023.05.001 |
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2023.11.001 |
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2025.01.001 |
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2023.11.001 |
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2023.11.001-noopenmp |
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2023.11.001 |
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ELSI
ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.
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2.11.0-PEXSI |
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EMBOSS
EMBOSS is 'The European Molecular Biology Open Software Suite' . EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
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6.6.0 |
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EPANET
EPANET is a software application used throughout the world to model water distribution systems.
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2.2.0 |
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EXP-T
The EXP-T program package is designed for high-precision modeling of molecular electronic structure using the relativistic Fock space multireference coupled cluster method (FS-RCC).
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e3753ab |
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1.8.4 |
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1.8.5 |
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e3753ab |
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EasyVVUQ
The aim of EasyVVUQ is to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.
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1.2 |
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Eigen
Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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3.4.0 |
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3.4.0 |
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Emacs
GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
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29.1 |
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FFTW
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
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3.3.10 |
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3.3.10 |
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3.3.10 |
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FFTW.MPI
FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
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3.3.10 |
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3.3.10 |
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FFmpeg
A complete, cross-platform solution to record, convert and stream audio and video.
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6.0 |
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FLAC
FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality.
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1.4.2 |
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FLTK
FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
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1.3.9 |
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Flask
Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors
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3.0.0 |
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FlexiBLAS
FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it.
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3.3.1 |
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3.4.4 |
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FriBidi
The Free Implementation of the Unicode Bidirectional Algorithm.
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1.0.13 |
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GAMESS-US
The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package.
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2024.2 |
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GATK
The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
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4.5.0.0-Java-21.0.2 |
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4.5.0.0-Java-21 |
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4.6.2.0-Java-17 |
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GCC
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
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13.2.0 |
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13.3.0 |
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GCCcore
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
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13.2.0 |
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13.3.0 |
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GDB
The GNU Project Debugger
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13.2 |
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GDCM
Grassroots DICOM: Cross-platform DICOM implementation
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3.0.21 |
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GL2PS
GL2PS: an OpenGL to PostScript printing library
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1.4.2 |
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GLM
OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications.
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0.9.9.8 |
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GLPK
The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
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5.0 |
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GLib
GLib is one of the base libraries of the GTK+ project
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2.78.1 |
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GMAP-GSNAP
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
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2023-04-20 |
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GMP
GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
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6.3.0 |
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GObject-Introspection
GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
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1.78.1 |
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GROMACS
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. This is a GPU enabled build, containing both MPI and threadMPI binaries.
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2024.3-CP2K-2025.1 |
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2025.1 |
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2021.4-PLUMED-2.7.6 |
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2024.1 |
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2024.3-PLUMED-2.9.3 |
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2024.1 |
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2025.1 |
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GSL
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
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2.7 |
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2.7 |
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GTK3
GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.
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3.24.39 |
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Gaussian
No description available
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g16.C.01 |
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Gdk-Pixbuf
The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
Versions | Environment loading command (via Lmod) |
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2.42.10 |
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Geant4
Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.
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11.1.3 |
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11.2.2 |
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Geant4-data
Datasets for Geant4.
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11.1.3 |
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11.2.2 |
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Ghostscript
Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
Versions | Environment loading command (via Lmod) |
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10.02.1 |
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GlobalArrays
Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model
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5.8.2 |
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Go
Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
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1.22.1 |
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1.23.6 |
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GraphicsMagick
GraphicsMagick is the swiss army knife of image processing.
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1.3.45 |
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Greenlet
The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs.
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3.0.3 |
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H5Part
H5part (HDF5 Particle Parallel I/O Library)
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1.6.5 |
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HAlign
HAlign 3: Fast multiple alignment of ultra-large numbers of similar DNA/RNA sequences
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3.0.0-Java-21.0.2 |
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HDF5
HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
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1.14.3-threadsafe |
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1.14.3-serial |
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1.14.3 |
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1.10.11 |
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1.14.3 |
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1.14.3 |
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1.8.12 |
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1.14.3 |
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1.14.3 |
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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).
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2.2.1 |
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HMMER
HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
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3.3.2 |
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3.4 |
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HTSlib
A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
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1.19.1 |
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HarfBuzz
HarfBuzz is an OpenType text shaping engine.
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8.2.2 |
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Hypre
Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences.
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2.31.0 |
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2.6.0b |
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2.31.0 |
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ICU
ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
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74.1 |
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75.1 |
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IPython
IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
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8.17.2 |
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IQ-TREE
Efficient phylogenomic software by maximum likelihood
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2.2.2.7 |
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ISA-L
Intelligent Storage Acceleration Library
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2.31.0 |
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ISL
isl is a library for manipulating sets and relations of integer points bounded by linear constraints.
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0.26 |
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ImageMagick
ImageMagick is a software suite to create, edit, compose, or convert bitmap images
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7.1.1-34 |
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Imath
Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics
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3.1.9 |
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Infernal
Infernal ("INFERence of RNA ALignment
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1.1.5 |
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Inspector
Intel Inspector is a dynamic memory and threading error checking tool for users developing serial and parallel applications
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2023.2.0 |
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JasPer
The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
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4.0.0 |
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Java
Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
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11.0.27 |
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17.0.15 |
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21.0.2 |
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Jellyfish
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
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2.3.0 |
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Judy
A C library that implements a dynamic array.
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1.0.5 |
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Julia
Julia is a high-level, high-performance dynamic programming language for numerical computing
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1.11.6-linux-x86_64 |
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Jupyter-bundle
This bundle collects a range of Jupyter interfaces (Lab, Notebook and nbclassic), extensions (Jupyter Server Proxy, Jupyter Resource Monitor, Jupyter Lmod) and the JupyterHub.
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20240522 |
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JupyterHub
JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.
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4.1.5 |
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JupyterLab
JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.
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4.2.0 |
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JupyterNotebook
The Jupyter Notebook is the original web application for creating and sharing computational documents. It offers a simple, streamlined, document-centric experience.
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7.2.0 |
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KAT
The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.
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2.4.2-Python-3.11.5 |
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KaHIP
The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.
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3.16 |
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LAME
LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
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3.100 |
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LAMMPS
LAMMPS Molecular Dynamics Simulator
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27Jun2024 |
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29Aug2024 |
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29Aug2024_update1 |
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LLVM
The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR
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14.0.6-llvmlite |
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16.0.6 |
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LMDB
LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
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0.9.31 |
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LSD2
Least-squares methods to estimate rates and dates from phylogenies
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2.4.1 |
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LZO
Portable lossless data compression library
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2.10 |
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Leptonica
Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications.
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1.85.0 |
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LibTIFF
tiff: Library and tools for reading and writing TIFF data files
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4.6.0 |
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Libint
Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.
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2.7.2-lmax-6-cp2k |
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2.7.2-lmax-6-cp2k |
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LittleCMS
Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
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2.15 |
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LocARNA
LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure.
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1.9.2.3 |
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Lua
Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
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5.4.6 |
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5.3.5 |
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LuaRocks
LuaRocks is the package manager for Lua modules. It allows you to create and install Lua modules as self-contained packages called rocks.
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3.11.1 |
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M4
GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
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1.4.19 |
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1.4.19 |
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1.4.18 |
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1.4.19 |
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MATIO
matio is an C library for reading and writing Matlab MAT files.
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1.5.26 |
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MATLAB
MATLAB: The Language of Technical Computing
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R2024b |
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MEGAHIT
An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
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1.2.9 |
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METIS
METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
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5.1.0 |
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MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
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17-b804f |
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MPC
Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal.
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1.3.1 |
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MPFR
The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
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4.2.1 |
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MUMPS
A parallel sparse direct solver
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5.6.1-metis |
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5.7.2-parmetis |
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5.7.2-parmetis |
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MVAPICH
This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH.
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3.0-threadsafe |
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3.0 |
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3.0 |
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Mako
A super-fast templating language that borrows the best ideas from the existing templating languages
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1.2.4 |
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MariaDB
MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
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11.6.0 |
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Mathematica
Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields.
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14.1 |
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Mesa
Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
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23.1.9 |
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Meson
Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
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1.2.3 |
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1.4.0 |
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1.4.0 |
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MetaEuk
MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.
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6 |
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MinIO-Client
MinIO Client (mc) provides a modern alternative to UNIX commands like ls, cat, cp, mirror, diff, find etc. It supports filesystems and Amazon S3 compatible cloud storage service (AWS Signature v2 and v4).
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2024-07-31T15-58-33Z |
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2025-02-04T04-57-50Z |
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Miniconda3
Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.
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23.9.0-0 |
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Molpro
Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
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mpp-2024.3.0.linux_x86_64_mpipr |
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NASM
NASM: General-purpose x86 assembler
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2.16.01 |
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NCIPLOT
NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient.
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4.2-20221021 |
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NSPR
Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
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4.35 |
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NSS
Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
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3.94 |
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NTPoly
is a massively parallel library for computing the functions of sparse, symmetric matrices based on polynomial expansions. For sufficiently sparse matrices, most of the matrix functions in NTPoly can be computed in linear time.
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3.1.0 |
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Nextflow
Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data
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24.10.2 |
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Ninja
Ninja is a small build system with a focus on speed.
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1.11.1 |
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1.12.1 |
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ORCA
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
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5.0.4 |
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6.0.0 |
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6.0.1 |
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6.1.0 |
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OSU-Micro-Benchmarks
OSU Micro-Benchmarks
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7.4 |
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7.4 |
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7.4 |
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Octave
GNU Octave is a high-level interpreted language, primarily intended for numerical computations.
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9.4.0 |
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OpenBLAS
OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
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0.3.24-ILP64 |
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0.3.24 |
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0.3.27 |
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OpenBabel
Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
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3.1.1 |
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OpenEXR
OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications
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3.2.0 |
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OpenFOAM
OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics.
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v2406 |
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OpenJPEG
OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.
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2.5.0 |
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OpenMPI
The Open MPI Project is an open source MPI-3 implementation.
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5.0.3 |
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5.0.3 |
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5.0.3 |
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OpenPGM
OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
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5.2.122 |
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OpenSSL
The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
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1.1 |
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3 |
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OpenTOPAS
TOPAS: Tool for Particle Simulation
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4.0.0 |
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PCRE
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
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8.45 |
|
PCRE2
The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
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10.42 |
|
PETSc
PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations.
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3.23.3 |
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3.23.3-debug |
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3.23.3 |
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PLUMED
PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes.
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2.9.0 |
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2.9.3 |
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2.7.6 |
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2.9.0 |
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2.9.3 |
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PMIx
Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability.
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5.0.3 |
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POV-Ray
The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports.
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3.7.0.10 |
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Pango
Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
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1.51.0 |
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ParMETIS
ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.
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4.0.3 |
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4.0.3 |
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ParaView
ParaView is a scientific parallel visualizer.
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5.12.0 |
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Peridigm
Peridigm is an open-source computational peridynamics code developed at Sandia National Laboratories for massively-parallel multi-physics simulations.
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1.5.4-82c6ad8 |
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Perl
Larry Wall's Practical Extraction and Report Language Includes a small selection of extra CPAN packages for core functionality.
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5.38.0 |
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5.38.2 |
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Perl-bundle-CPAN
A set of common packages from CPAN
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5.38.0 |
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Pillow
Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
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10.2.0 |
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PnetCDF
Parallel netCDF: A Parallel I/O Library for NetCDF File Access
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1.12.3 |
|
1.12.3 |
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PostgreSQL
PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
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16.1 |
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PrgEnv-cray
No description available
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8.5 |
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PyYAML
PyYAML is a YAML parser and emitter for the Python programming language.
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6.0.1 |
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PyZMQ
Python bindings for ZeroMQ
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25.1.2 |
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PycURL
PycURL is a Python interface to libcurl. PycURL can be used to fetch objects identified by a URL from a Python program, similar to the urllib Python module. PycURL is mature, very fast, and supports a lot of features.
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7.45.3 |
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Python
Python is a programming language that lets you work more quickly and integrate your systems more effectively.
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3.11.5 |
|
3.12.3 |
|
Python-bundle-PyPI
Bundle of Python packages from PyPI
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2023.10 |
|
2024.06 |
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Q-Chem
Q-Chem 6.2
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6.2-smp |
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6.3-smp |
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Qhull
Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull.
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2020.2 |
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Qt5
Qt is a comprehensive cross-platform C++ application framework.
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5.15.13 |
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Qt6
Qt is a comprehensive cross-platform C++ application framework.
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6.6.3 |
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QuantumESPRESSO
Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft).
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6.7 |
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7.3.1 |
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7.5 |
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6.7 |
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7.3 |
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7.3-nsx-50 |
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Qwt
The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background.
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6.3.0 |
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R
R is a free software environment for statistical computing and graphics.
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4.3.3 |
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4.5.1 |
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ROOT
The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.
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6.28.12 |
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6.30.06 |
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6.32.04 |
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RSEM
RNA-Seq by Expectation-Maximization
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1.3.3 |
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RapidJSON
A fast JSON parser/generator for C++ with both SAX/DOM style API
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1.1.0-20240409 |
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Rcorrector
Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
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1.0.2 |
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Ruby
Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
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3.4.2 |
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Rust
Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
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1.73.0 |
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1.76.0 |
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1.78.0 |
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S-Lang
S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on.
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2.3.0 |
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SAMtools
SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
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1.19.2 |
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SCOTCH
Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.
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7.0.4 |
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7.0.4 |
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SDL2
SDL: Simple DirectMedia Layer, a cross-platform multimedia library
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2.28.5 |
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SEPP
SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
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4.5.1 |
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SLEPc
SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.
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3.23.1 |
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3.23.1 |
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SPLA
No description available
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1.6.1 |
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1.5.5 |
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SQLAlchemy
SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives application developers the full power and flexibility of SQL. SQLAlchemy provides a full suite of well known enterprise-level persistence patterns, designed for efficient and high-performing database access, adapted into a simple and Pythonic domain language.
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2.0.29 |
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SQLite
SQLite: SQL Database Engine in a C Library
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3.43.1 |
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3.45.3 |
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SRA-Toolkit
The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
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3.1.1 |
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STAR
STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
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2.7.11b |
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STRUMPACK
STRUMPACK - STRUctured Matrix PACKage - Fast linear solvers and preconditioner for both dense and sparse systems using low-rank structured factorization with randomized sampling.
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7.1.0 |
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8.0.0 |
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7.1.0 |
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8.0.0 |
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SUNDIALS
SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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6.3.0 |
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SWIG
SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
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4.1.1 |
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Salmon
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimate from RNA-seq data.
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1.10.3 |
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ScaLAPACK
The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
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2.2.0-fb |
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SciPy-bundle
Bundle of Python packages for scientific software
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2023.11 |
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2024.05 |
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2023.11 |
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Simple-DFTD3
Reimplementation of the D3 dispersion correction. The s-dftd3 project aims to provide a user-friendly and uniform interface to the D3 dispersion model and for the calculation of DFT-D3 dispersion corrections.
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1.2.1 |
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1.2.1 |
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SuiteSparse
SuiteSparse is a collection of libraries to manipulate sparse matrices.
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7.7.0 |
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7.7.0 |
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5.13.0-METIS-5.1.0 |
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7.1.0 |
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7.1.0-METIS-5.1.0 |
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SuperLU_DIST
SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines.
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8.2.1 |
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8.2.1 |
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Szip
Szip compression software, providing lossless compression of scientific data
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2.1.1 |
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2.1.1 |
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TOML-Fortran
TOML parser for Fortran projects
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0.4.2 |
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0.4.2 |
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TOPAS
TOPAS wraps and extends the Geant4 Simulation Toolkit to make advanced Monte Carlo simulation of all forms of radiotherapy easier to use for medical physicists.
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3.9 |
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TRAVIS
TRAVIS is a free tool for analyzing and visualizing trajectories from all kinds of Molecular Dynamics or Monte Carlo simulations. It is intended to be easy to install and easy to use.
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220729 |
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TURBOMOLE
TURBOMOLE v 7.9 quantum chemistry chemistry package, SMP version
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7.9-SMP |
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Tcl
Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.
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8.6.13 |
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8.6.14 |
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8.6.13 |
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TheoDORE
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a program suite for the analysis of excited states obtained from quantum chemical excited state calculations.
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3.2 |
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Tk
Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
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8.6.13 |
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Tkinter
Tkinter module, built with the Python buildsystem
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3.11.5 |
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Trilinos
The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages.
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13.4.0-Python-3.11.5 |
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16.1.0-Python-3.11.5 |
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Trimmomatic
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
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0.39-Java-21.0.2 |
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Trinity
Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
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2.15.1 |
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Uintah
The Uintah software suite is a set of libraries and applications for simulating and analyzing complex chemical and physical reactions.
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516079d |
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UnZip
UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles
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6.0 |
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6.0 |
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VASP
The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
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6.4.3 |
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6.4.3-no-HDF5 |
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6.5.1 |
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5.4.4-DSCF |
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5.4.4 |
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5.4.4-vaspsol-vtst |
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6.4.2-vtst |
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6.4.3-Dsingle_prec_bse |
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6.4.3-ELPA-Dsingle_prec_bse |
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6.4.3 |
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6.5.1-Dsingle_prec_bse |
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6.5.1 |
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6.3.2-vaspsol-vtst |
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6.4.2-vtst |
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6.4.3 |
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6.5.1-Dsingle_prec_bse |
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6.4.3 |
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VMD
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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1.9.4a57 |
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VSCode
Visual Studio Code is a lightweight but powerful source code editor which runs on your desktop and is available for Windows, macOS and Linux. It comes with built-in support for JavaScript, TypeScript and Node.js and has a rich ecosystem of extensions for other languages and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin your journey with VS Code with these introductory videos.
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1.100 |
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VTK
The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
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9.0.0 |
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9.3.0 |
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9.5.0 |
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VTune
Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java.
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2023.2.0 |
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ViennaRNA
The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
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2.5.0 |
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2.6.4 |
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Visit
VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool. From Unix, Windows or Mac workstations, users can interactively visualize and analyze data ranging in scale from small (105 core) leadership-class computing facility simulation campaigns. Users can quickly generate visualizations, animate them through time, manipulate them with a variety of operators and mathematical expressions, and save the resulting images and animations for presentations. VisIt contains a rich set of visualization features to enable users to view a wide variety of data including scalar and vector fields defined on two- and three-dimensional (2D and 3D) structured, adaptive and unstructured meshes. Owing to its customizeable plugin design, VisIt is capabable of visualizing data from over 120 different scientific data formats.
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3.4.9-01f068f |
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Wannier90
A tool for obtaining maximally-localised Wannier functions
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3.1.0 |
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2.1.0 |
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3.1.0 |
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3.1.0 |
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3.1.0 |
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3.1.0 |
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Wayland
Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers.
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1.22.0 |
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X11
The X Window System (X11) is a windowing system for bitmap displays
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20231019 |
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XZ
xz: XZ utilities
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5.4.4 |
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5.4.5 |
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Xerces-C++
Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
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3.2.5 |
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Yambo
Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.
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5.2.4-slepc |
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Yasm
Yasm: Complete rewrite of the NASM assembler with BSD license
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1.3.0 |
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ZeroMQ
ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
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4.3.5 |
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aiohttp
Asynchronous HTTP client/server framework for asyncio and Python.
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3.9.5 |
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alsa-lib
The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality to the Linux operating system.
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1.2.11 |
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1.2.8 |
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amd
AMD Optimizing C Compiler (AOCC) based compiler toolchain, including OpenMPI for MPI support and AOCL libraries.
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2023b |
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ant
Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
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1.10.14-Java-21 |
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antiword
Antiword: a free MS Word document reader
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0.37 |
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aompi
AOCC based compiler toolchain, including OpenMPI for MPI support.
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2023b |
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arpack-ng
ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
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3.9.0 |
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3.9.1 |
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3.9.0 |
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assimp
Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data.
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5.3.1 |
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asyncssh
AsyncSSH is a Python package which provides an asynchronous client and server implementation of the SSHv2 protocol on top of the Python 3.6+ asyncio framework.
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2.14.2 |
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at-spi2-atk
AT-SPI 2 toolkit bridge
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2.38.0 |
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at-spi2-core
Assistive Technology Service Provider Interface.
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2.50.0 |
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bcrypt
Acceptable password hashing for your software and your servers (but you should really use argon2id or scrypt)
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4.1.3 |
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binutils
binutils: GNU binary utilities
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2.40 |
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2.42 |
|
2.40 |
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2.42 |
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bokeh
Statistical and novel interactive HTML plots for Python
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3.4.1 |
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btllib
Bioinformatics Technology Lab common code library
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1.7.0 |
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bwakit
Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.
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0.7.15_x64-linux |
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bzip2
bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
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1.0.8 |
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1.0.8 |
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1.0.8 |
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cURL
libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
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8.3.0 |
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8.7.1 |
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8.0.1 |
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cairo
Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
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1.18.0 |
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cce
No description available
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17.0 |
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cffi
C Foreign Function Interface for Python. Interact with almost any C code from Python, based on C-like declarations that you can often copy-paste from header files or documentation.
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1.15.1 |
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1.16.0 |
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configurable-http-proxy
HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server.
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4.6.1 |
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cpe
No description available
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23 |
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cpio
The cpio package contains tools for archiving.
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2.15 |
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cppy
A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations.
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1.2.1 |
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cray-fftw
No description available
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3.3.10 |
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cray-libsci
No description available
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23.12 |
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cray-mpich
No description available
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8.1 |
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cryptography
cryptography is a package designed to expose cryptographic primitives and recipes to Python developers.
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41.0.5 |
|
42.0.8 |
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cuDNN
The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
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8.9.7.29-CUDA-12.4.0 |
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dask
Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
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2024.5.1 |
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dftd4
This is a repackaged version of the DFTD3 program by S. Grimme and his coworkers. The original program (V3.1 Rev 1) was downloaded at 2016-04-03. It has been converted to free format and encapsulated into modules.
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3.4.0 |
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3.7.0 |
|
3.4.0 |
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3.7.0 |
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3.4.0 |
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dialog
A utility for creating TTY dialog boxes
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1.3-20240619 |
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dotNET-Core
.NET is a free, cross-platform, open source developer platform for building many different types of applications. With .NET, you can use multiple languages, editors, and libraries to build for web, mobile, desktop, gaming, and IoT. Contains the SDK and the Runtime.
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9.0.305 |
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double-conversion
Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
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3.3.0 |
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eT
eT is an open source program with coupled cluster, multiscale and multilevel methods
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1.9.13 |
|
expat
Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags).
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2.5.0 |
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2.6.2 |
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fastp
A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
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0.23.4 |
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ffmpeg-python
Python bindings for FFmpeg - with complex filtering support
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0.2.0 |
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ffnvcodec
FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically).
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12.1.14.0 |
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file
The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains.
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5.43 |
|
flex
Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
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2.6.4 |
|
2.6.4 |
|
2.6.4 |
|
flit
A simple packaging tool for simple packages.
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3.9.0 |
|
3.9.0 |
|
flook
The fortran-Lua-hook library.
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0.8.4 |
|
0.8.4 |
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fontconfig
Fontconfig is a library designed to provide system-wide font configuration, customization and application access.
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2.14.2 |
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foss
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
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2023b |
|
freeglut
freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
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3.4.0 |
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freetype
FreeType 2 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 graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
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2.13.2 |
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gawk
The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code.
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5.3.0 |
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gettext
GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
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0.22 |
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0.22.5 |
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0.19.8.1 |
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0.22.5 |
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0.22 |
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gfbf
GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.
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2023b |
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2024a |
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giflib
giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
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5.2.1 |
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gimkl
GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL
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2023b |
|
git
Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
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2.42.0 |
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2.45.1 |
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gmkl
GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL
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2023b |
|
gnupg-bundle
GnuPG — The Universal Crypto Engine
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20240306 |
|
gnuplot
Portable interactive, function plotting utility
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5.4.8 |
|
gomkl
GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL
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2023b |
|
gompi
GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
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2023b |
|
gperf
GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
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3.1 |
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graphite2
Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world.
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1.3.14 |
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groff
Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output.
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1.23.0 |
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gzip
gzip (GNU zip) is a popular data compression program as a replacement for compress
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1.13 |
|
1.13 |
|
h5py
HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
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3.11.0 |
|
3.11.0 |
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hatch-jupyter-builder
Hatch Jupyter Builder is a plugin for the hatchling Python build backend. It is primarily targeted for package authors who are providing JavaScript as part of their Python packages. Typical use cases are Jupyter Lab Extensions and Jupyter Widgets.
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0.9.1 |
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hatchling
Extensible, standards compliant build backend used by Hatch, a modern, extensible Python project manager.
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1.18.0 |
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1.24.2 |
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help2man
help2man produces simple manual pages from the '--help' and '--version' output of other commands.
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1.49.3 |
|
1.49.3 |
|
htop
An interactive process viewer for Unix
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3.3.0 |
|
hwloc
The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.
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2.9.2 |
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hypothesis
Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
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6.90.0 |
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6.103.1 |
|
iimkl
Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).
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2023b |
|
iimpi
Intel C/C++ and Fortran compilers, alongside Intel MPI.
Versions | Environment loading command (via Lmod) |
---|---|
2023b |
|
imkl
Intel oneAPI Math Kernel Library
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2023.2.0 |
|
2024.0.0 |
|
imkl-FFTW
FFTW interfaces using Intel oneAPI Math Kernel Library
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2023.2.0 |
|
impi
Intel MPI Library, compatible with MPICH ABI
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2021.10.0 |
|
2021.10.0 |
|
2021.13.1 |
|
intel
Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL).
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2023b |
|
intel-compilers
Intel C, C++ & Fortran compilers (classic and oneAPI)
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2023.2.1 |
|
2024.2.0 |
|
intltool
intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
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0.51.0 |
|
iomkl
Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL).
Versions | Environment loading command (via Lmod) |
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2023b |
|
iompi
Intel C/C++ and Fortran compilers, alongside Open MPI.
Versions | Environment loading command (via Lmod) |
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2023b |
|
itac
The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays.
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2021.10.0 |
|
jbig2enc
JBIG2 encodes bi-level (1 bpp) images using a number of clever tricks to get better compression than G4.
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0.30 |
|
jbigkit
JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
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2.1 |
|
jdftx
JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use.
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1.7.0 |
|
jedi
Jedi - an awesome autocompletion, static analysis and refactoring library for Python.
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0.19.1 |
|
jemalloc
jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
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5.3.0 |
|
json-c
JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
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0.17 |
|
0.13 |
|
json-fortran
JSON-Fortran: A Modern Fortran JSON API
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9.0.2 |
|
9.0.2 |
|
jupyter-resource-usage
Jupyter Notebook Extension for monitoring your own Resource Usage (memory and/or CPU)
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1.0.2 |
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jupyter-server
The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila.
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2.14.0 |
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jupyter-server-proxy
Jupyter Server Proxy lets you run arbitrary external processes (such as RStudio, Shiny Server, Syncthing, PostgreSQL, Code Server, etc) alongside your notebook server and provide authenticated web access to them using a path like /rstudio next to others like /lab. Alongside the python package that provides the main functionality, the JupyterLab extension (@jupyterlab/server-proxy) provides buttons in the JupyterLab launcher window to get to RStudio for example.
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4.1.2 |
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jupyterlab_nvdashboard
NVDashboard is a JupyterLab extension for displaying GPU usage dashboards. It enables JupyterLab users to visualize system hardware metrics within the same interactive environment they use for development. Supported metrics include: GPU-compute utilization, GPU-memory consumption, PCIe throughput and NVLink throughput
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0.11.0 |
|
jupyterlmod
Jupyter interactive notebook server extension that allows users to interact with environment modules before launching kernels. The extension uses Lmod's Python interface to accomplish module-related tasks like loading, unloading, saving collections, etc.
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5.2.1 |
|
kallisto
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
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0.50.1 |
|
koala
No description available
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1.0 |
|
libAfterImage
libAfterImage is a generic image manipulation library. It was initially implemented to address AfterStep Window Manager's needs for image handling, but it evolved into extremely powerful and flexible software, suitable for virtually any project that has needs for loading, manipulating, displaying images, as well as writing images in files.
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1.20 |
|
libGLU
The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
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9.0.3 |
|
libGridXC
A library to compute the exchange and correlation energy and potential in spherical (i.e. atoms) or periodic systems.
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2.0.2 |
|
2.0.2 |
|
libPSML
A library to handle pseudopotentials in PSML format
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2.1.0 |
|
2.1.0 |
|
libaio
Asynchronous input/output library that uses the kernels native interface.
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0.3.113 |
|
libarchive
Multi-format archive and compression library
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3.7.2 |
|
3.7.4 |
|
3.6.2 |
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libcerf
libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
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2.3 |
|
libdeflate
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.
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1.19 |
|
libdrm
Direct Rendering Manager runtime library.
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2.4.117 |
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libepoxy
Epoxy is a library for handling OpenGL function pointer management for you
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1.5.10 |
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libevent
The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
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2.1.12 |
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libfabric
Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.
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1.15.2.0 |
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libfdf
LibFDF is the official implementation of the FDF specifications for use in client codes.
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0.5.1 |
|
0.5.1 |
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libffi
The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
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3.4.4 |
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3.4.5 |
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3.2.1 |
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libgd
GD is an open source code library for the dynamic creation of images by programmers.
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2.3.3 |
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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.
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1.7.2 |
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libglvnd
libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
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1.7.0 |
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libharu
libHaru is a free, cross platform, open source library for generating PDF files.
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2.3.0 |
|
2.3.0 |
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libiconv
Libiconv converts from one character encoding to another through Unicode conversion
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1.17 |
|
1.17 |
|
libjpeg-turbo
libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
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3.0.1 |
|
libmbd
Libmbd implements the many-body dispersion (MBD) method in several programming languages and frameworks: - The Fortran implementation is the reference, most advanced implementation, with support for analytical gradients and distributed parallelism, and additional functionality beyond the MBD method itself. It provides a low-level and a high-level Fortran API, as well as a C API. Furthermore, Python bindings to the C API are provided. - The Python/Numpy implementation is intended for prototyping, and as a high-level language reference. - The Python/Tensorflow implementation is an experiment that should enable rapid prototyping of machine learning applications with MBD. The Python-based implementations as well as Python bindings to the Libmbd C API are accessible from the Python package called Pymbd.
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0.12.6 |
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libnsl
The libnsl package contains the public client interface for NIS(YP).
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1.3.0 |
|
libogg
Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs.
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1.3.5 |
|
libopus
Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec.
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1.4 |
|
libpciaccess
Generic PCI access library.
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0.17 |
|
libpng
libpng is the official PNG reference library
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1.6.40 |
|
1.2.59 |
|
libreadline
The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
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8.2 |
|
8.2 |
|
7.0 |
|
8.0 |
|
8.2 |
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libsndfile
Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
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1.2.2 |
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libsodium
Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
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1.0.19 |
|
libtirpc
Libtirpc is a port of Suns Transport-Independent RPC library to Linux.
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1.3.3 |
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libtool
GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.
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2.4.7 |
|
2.4.7 |
|
2.4.7 |
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libunwind
The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
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1.6.2 |
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libvorbis
Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format
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1.3.7 |
|
libvori
C++ library implementing the Voronoi integration as well as the compressed bqb file format. The present version of libvori is a very early development version, which is hard-coded to work with the CP2k program package.
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220621 |
|
libwebp
WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.
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1.3.2 |
|
libxc
Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.
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6.2.2-disable-fhc |
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5.1.6 |
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6.2.2-disable-fhc |
|
6.2.2 |
|
5.1.6 |
|
6.2.2-disable-fhc |
|
6.2.2 |
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libxml2
Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
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2.11.5 |
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2.12.7 |
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2.9.10 |
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libxslt
Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
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1.1.38 |
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libxsmm
LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86).
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1.17 |
|
1.17 |
|
libyaml
LibYAML is a YAML parser and emitter written in C.
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0.2.5 |
|
linaro-forge
Linaro Forge combines Linaro DDT, the leading debugger for time-saving high performance application debugging, Linaro MAP, the trusted performance profiler for invaluable optimization advice across native and Python HPC codes, and Linaro Performance Reports for advanced reporting capabilities.
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24.0.4 |
|
lpsolve
Mixed Integer Linear Programming (MILP) solver
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5.5.2.11 |
|
lurk
lurk is a simple and pretty alternative to strace
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0.3.10 |
|
lxml
The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.
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4.9.3 |
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lz4
LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
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1.9.4 |
|
1.9.4 |
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maeparser
maeparser is a parser for Schrodinger Maestro files.
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1.3.1 |
|
magma
The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.
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2.7.2-CUDA-12.4.0 |
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make
GNU version of make utility
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4.4.1 |
|
4.4.1 |
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makeinfo
makeinfo is part of the Texinfo project, the official documentation format of the GNU project.
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7.1 |
|
matplotlib
matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
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3.8.2 |
|
3.8.2 |
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maturin
This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building wheels for python 3.5+ on windows, linux, mac and freebsd, can upload them to pypi and has basic pypy and graalpy support.
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1.3.1 |
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1.5.0-Rust-1.76.0 |
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1.6.0 |
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mcpartools
mcpartools is a software simplifying time consuming simulation of particle transport using Monte Carlo codes (Fluka, SHIELDHIT12A).
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0.6.2-Python-3.11.5 |
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mctc-lib
Common tool chain for working with molecular structure data in various applications. This library provides a unified way to perform operations on molecular structure data, like reading and writing to common geometry file formats.
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0.3.1 |
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0.3.2 |
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0.3.1 |
|
0.3.2 |
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meson-python
Python build backend (PEP 517) for Meson projects
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0.15.0 |
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0.16.0 |
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0.16.0 |
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mgltools
The MGLTools software suite can be used for visualization and analysis of molecular structures and comprises the Python Molecular Viewer (PMV, a general purpose molecular viewer), AutoDockTools (ADT, a set of PMV commands specifically developed to support AutoDock users) and Vision (a visual programming environment).
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1.5.7 |
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miniprot
Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift.
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0.13 |
|
mold
mold is a high-performance drop-in replacement for existing Unix linkers.
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2.3.1 |
|
mpg123
Fast console MPEG Audio Player and decoder library
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1.32.10 |
|
mpi4py
MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.
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3.1.5 |
|
3.1.5 |
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mstore
Molecular structure store for testing
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0.3.0 |
|
0.3.0 |
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multicharge
Electronegativity equilibration model for atomic partial charges.
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0.3.0 |
|
0.3.0 |
|
nbclassic
NbClassic provides a backwards compatible Jupyter Notebook interface that you can install side-by-side with the latest versions: That way, you can fearlessly upgrade without worrying about your classic extensions and customizations breaking.
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1.0.0 |
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ncbi-vdb
The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
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3.1.1 |
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ncurses
The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
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6.4 |
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6.5 |
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6.0 |
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6.1 |
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6.3 |
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6.4 |
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6.5 |
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netCDF
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
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4.9.2 |
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4.9.2 |
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netCDF-Fortran
NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
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4.6.1 |
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4.6.1 |
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networkx
NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
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3.2.1 |
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nodejs
Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
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20.9.0 |
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numactl
The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
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2.0.16 |
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numba
Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
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0.58.1 |
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p7zip
p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
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17.04 |
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parallel
parallel: Build and execute shell commands in parallel
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20240322 |
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patchelf
PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.
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0.18.0 |
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0.18.0 |
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picard
A set of tools (in Java) for working with next generation sequencing data in the BAM format.
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2.25.1-Java-21 |
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pixman
Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
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0.42.2 |
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pkg-config
pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).
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0.29.2 |
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pkgconf
pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org.
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2.0.3 |
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2.2.0 |
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1.8.0 |
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poetry
Python packaging and dependency management made easy. Poetry helps you declare, manage and install dependencies of Python projects, ensuring you have the right stack everywhere.
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1.6.1 |
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1.8.3 |
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1.8.3 |
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poppler
Poppler is a PDF rendering library
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24.04.0 |
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prodigal
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
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2.6.3 |
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psi4
PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel.
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1.9.1 |
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pstack
JSON-C implements a reference counting object model that allows you to easily construct JSON objects in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON objects.
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2.14 |
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psycopg
Psycopg is the most popular PostgreSQL adapter for the Python programming language.
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3.1.18 |
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pybind11
pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
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2.12.0 |
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2.11.1 |
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pymchelper
pymchelper is a toolkit for aiding users of the particle transport codes, such as FLUKA and SHIELD-HIT12A.
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2.7.2-Python-3.11.5 |
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qrupdate
qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.
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1.1.2 |
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rclone
Rclone is a command line program to sync files and directories to and from a variety of online storage services
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1.67.0 |
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re2c
re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
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3.1 |
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ruamel.yaml
ruamel.yaml is a YAML 1.2 loader/dumper package for Python.
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0.18.6 |
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scikit-build
Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.
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0.17.6 |
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0.17.6 |
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scikit-build-core
Scikit-build-core is a complete ground-up rewrite of scikit-build on top of modern packaging APIs. It provides a bridge between CMake and the Python build system, allowing you to make Python modules with CMake.
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0.9.3 |
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setuptools-rust
setuptools-rust is a plugin for setuptools to build Rust Python extensions implemented with PyO3 or rust-cpython.
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1.8.0 |
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1.9.0 |
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shieldhit
SHIELD-HIT12A is a Monte Carlo particle transport program which is modified for proton and heavy ion particle therapy research
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current |
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snappy
Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
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1.1.10 |
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sparsehash
An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed.
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2.0.4 |
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spglib
Spglib is a C library for finding and handling crystal symmetries.
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2.0.2 |
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spglib-python
Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.
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2.5.0 |
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tbb
Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability.
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2021.13.0 |
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tesseract
Tesseract is an optical character recognition engine
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5.5.0 |
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test-drive
This project offers a lightweight, procedural unit testing framework based on nothing but standard Fortran.
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0.5.0 |
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0.5.0 |
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texlive
TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
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20230313 |
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20250308 |
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tornado
Tornado is a Python web framework and asynchronous networking library.
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6.4 |
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typing-extensions
Typing Extensions - Backported and Experimental Type Hints for Python
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4.10.0 |
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unrtf
UnRTF is a command-line program written in C which converts documents in Rich Text Format (.rtf) to HTML, LaTeX, troff macros, and RTF itself.
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0.21.10 |
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util-linux
Set of Linux utilities
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2.39 |
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virtualenv
A tool for creating isolated virtual python environments.
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20.24.6 |
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20.26.2 |
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wise2
Wise2
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2.4.1 |
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x264
x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
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20231019 |
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x265
x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.
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3.5 |
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xmlf90
A fast XML parser and generator in Fortran
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1.6.3 |
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1.6.3 |
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xorg-macros
X.org macros utilities.
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1.20.0 |
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xprop
The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.
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1.2.7 |
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xtb
xtb - An extended tight-binding semi-empirical program package.
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6.7.1-ec4f388 |
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6.7.1 |
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6.6.1 |
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xxd
xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files.
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9.0.2112 |
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9.1.0307 |
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yaml-cpp
yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec
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0.8.0 |
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zlib
zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
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1.2.13 |
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1.3.1 |
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1.2.13 |
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1.3.1 |
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zsh
Zsh is a shell designed for interactive use, although it is also a powerful scripting language.
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5.9 |
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zstd
Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.
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1.5.5 |
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1.5.6 |
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Last update: October 4, 2025