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[TOC]

Physics and Engineering

  • CDO version (1.6.4) — CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.
  • CLHEP version (2.1.0.1,2.2.0.8,2.3.1.0,2.3.1.1,...) — Set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra.
  • CP2K version (2.5.1) — CP2K is the state-of-the-art method for accurate atomistic simulations.
  • EEMT version (0.1) — EEMT stack which includes a bunch of GIS tools
  • GDAL version (2.0.0) — GDAL is a translator library for raster and vector geospatial data formats that is released by the Open Source Geospatial Foundation.
  • GEANT4 version (9.4p02,10.02,10.3p01) — toolkit for the simulation of the passage of particles through matter.
  • GLPK version (4.54) — glpk is the GNU's linear programming took kit.
  • GNUPLOT version (4.6.5) — Gnuplot is an application for generating plots.
  • GRAPHVIZ version (2.38.0) — Graphviz is an application for visualizing networks and graphs.
  • GRASS version (6.4.4) — GRASS (Geographic Resources Analysis Support System)
  • JULIA version (0.6.0) — Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.
  • JULIA version (0.6.0) — Julia is a high-level, high-performance dynamic programming language for technical computing, with syntax that is familiar to users of other technical computing environments.
  • LAMMPS version (2.0,15May15) — LAMMPS is a particle simulator code.
  • LMOD version (5.6.2) — Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem.
  • LMOD version (AnEnvironmentModuleSystem) — Lmod is a Lua based module system that easily handles the MODULEPATH Hierarchical problem.
  • MADGRAPH version (2.1.2,2.2.2) — MadGraph is a monte carlo generator for particle physics interactions
  • MATLAB version (2013b,2014a,2014b,2015a,...) — Runtime libraries. The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
  • OCTAVE version (3.8.1) — Octave is a high-level interpreted language
  • OPENSEES version (6482) — OpenSees is a software framework for developing applications to simulate the performance of structural and geotechnical sys tems subjected to earthquakes.
  • PANDANA version (-) — PANDANA performs hundreds of thousands of network queries in under a second (for walking-scale distances)
  • PSIMS version (-) — A set of packages for needed for the PSIMS (numpy, h5py, netcdf4)
  • PYTORCH version (-) — PYTORCH Tensors and Dynamic neural networks in Python with strong GPU acceleration.
  • QHULL version (2012.1) — qhull libraries provide functions for computing convex hull.
  • R version (3.1.1,3.2.0,3.2.1,3.2.2,3.3.1,3.3.2) — R is a free software environment for statistical computing and graphics.
  • ROOT version (5.34-32-py34,5.34-32,6.06-02-py34) — ROOT is a high energy physics data analysis framework.
  • ROOT_NUMPY version (-) — ROOT_NUMPY is a Python extension module that provides an efficient interface between ROOT and NumPy
  • SIESTA version (3.2) — SIESTA performs efficient electronic structure calculations of molecules and solids.
  • UDUNITS version (2.2.17) — UDUNITS package supports units of physical quantities.

Chemistry and Biochemistry

  • ARC-LITE version (2015) — arc-lite (ARCIMBOLDO) is a package for the protein structure refinement.
  • AUTODOCK version (4.2.6) — Autodock is a suite of automated docking tools to predict how small molecules bind to a receptor.
  • CASINO version (2.13.211) — CASINO performs quantum Monte Carlo (QMC) electronic structure calculations.
  • CCP4 version (2015) — arc-lite (ARCIMBOLDO) is a package for the protein structure refinement.
  • ESPRESSO version (5.1,5.2) — Quantum Espresso is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale.
  • GAMESS version (2013) — GAMESS is a general ab initio quantum chemistry package.
  • GROMACS version (4.6.5,5.0.0,5.0.5.cuda,5.0.5,...) — Gromacs molecular dynamics simulator. Requires fftw/fftw-3.3.4-gromacs
  • NAMD version (2.9,2.10.cuda,2.10) — NAnoscale Molecular Dynamics (NAMD) program.
  • OPENBABEL version (2.3.2) — Open Babel is a chemical toolbox designed to speak the many languages of chemical data.
  • OPENBUGS version (3.2.3) — OpenBUGS is a software package for performing Bayesian inference Using Gibbs Sampling.
  • ORCA version (3.0.3,4.0.0) — ORCA is a general-purpose quantum chemistry program package.
  • PHENIX version (1.10) — software suite for the determination of molecular structures from X-Ray and other methods.
  • PSI4 version (0.3.74,1.1) — Psi4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties.
  • ROSETTA version (2015,2016-02,2016-32) — The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
  • SHELX version (2015) — SHELX is a set of programs for the determination of small and macromolecular crystal structures.
  • SHELX version (2015) — SHELX is a set of programs for the determination of small and macromolecular crystal structures.
  • SIMBODY version (3.5.3) — Simbody is an open source software system for biomechanical modeling, simulation and analysis.
  • SQLITE version (3.8.11.1) — SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine.
  • VMD version (1.9.1) — VMD is a molecular dynamics visualization application.

Image Analysis

  • ANTS version (1.9.4,2.1.0) — ANTs is a popular toolkit for medical image registration and segmentation.
  • BLENDER version (-) — Blender 3D rendering software.
  • ELASTIX version (2015) — consists of a collection of algorithms that are commonly used to solve (medical) image registration problems
  • FIJI version (2.0) — Fiji is an image processing package. It can be described as a "batteries-included" distribution of ImageJ (and ImageJ2)
  • FREESURFER version (5.1.0,5.3.0,6.0.0) — Freesurfer is an open source software suite for processing and analyzing (human) brain MRI images.
  • FSL version (5.0.8) — FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data
  • GATE version (7.2) — Gate does simulations of preclinical and clinical scans in Emission Tomography, Transmission Tomography a nd Radiation Therapy.
  • IGRAPH version (0.7.1) — igraph is a library for creating and manipulating graphs.
  • IMAGEMAGICK version (7.0.2) — Imagemagick is a set of image manipulation tools.
  • IMAGE_MODULES version (-) — Image_modules includes a set of Python packages for needed for the image processing

Bioinformatics

  • ABYSS version (2.0.2) — ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads.
  • BEDTOOLS version (2.21) — A set of tools for a wide-range of genomics analysis tasks.
  • BLASR version (1.3.1) — Blasr is a tool to search and align sequences with refinements.
  • BLAST version (-) — Blast is a tool to search and align gene and protein sequences.
  • BOWTIE version (2.2.3,2.2.9) — Bowtie is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
  • BWA version (0.7.12,2014) — BWA is a package for mapping low-divergent sequences against a large reference genome.
  • CUFFLINKS version (2.2.1) — Cufflinks assembles transcripts
  • ENTROPY version (2017.03.16) — Admixture and the organization of genetic diversity in a butterfly species complex revealed through common and rare genetic variants.
  • ETE2 version (2.3.8) — ETE is a toolkit based on Python framework for the analysis and visualization of trees.
  • HISAT2 version (2.0.3-beta) — HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against th e general human population (as well as against a single reference genome).
  • HMMER version (3.1) — HMMER searches and aligns homologs of protein sequences using hidden Markov models.
  • MOTHUR version (1.39.0) — mothur is a project that seeks to develop a single piece of open-source, expandable software to fill the bioinformatics nee ds of the microbial ecology community.
  • MRBAYES version (3.2.2) — MrBayes is a program for Bayesian inference of phylogenetic and evolutionary models.
  • MUMMER version (3.23) — MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form
  • MUSCLE version (3.8.31) — MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation
  • NGSTOOLS version (2017.03.16) — ngsTools is a collection of programs for population genetics analyses from NGS data, taking into account its statistical un certainty.
  • PBSUITE version (14.9.9) — PBSuite is a software for long-read sequencing data from PacBio.
  • PRODIGAL version (2.6.3) — Fast, reliable protein-coding gene prediction for prokaryotic genomes.
  • RAXML version (8.2.9) — A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies
  • RAXML-NG version (0.5.0beta) — Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion.
  • SAMTOOLS version (0.1.17,1.3.1) — Samtools is a set of utilities for working with data in sequence alignment map format.
  • SEQGEN version (1.3.3) — Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny
  • SHRIMP version (2.2.3) — SHRiMP is a software package for aligning genomic reads against a target genome.
  • SRA version (2.5.4,2.8.0) — The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format
  • STRINGTIE version (1.1.2,1.2.2) — StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
  • TASSEL version (5.0) — TASSEL has functionality for association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization.
  • TOPHAT version (2.0.13,2.1.1) — TopHat is a fast splice junction mapper for RNA-Seq reads.
  • TRANSABYSS version (1.5.5) — de novo assembly of RNA-Seq data using ABySS
  • UCLUST version (2.22) — Uclust offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
  • VIENNARNA version (2.2) — ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

Numerical Libraries

  • ATLAS version (3.10.1,3.10.2) — The ATLAS (Automatically Tuned Linear Algebra Software) provides optimzied libraries for Linear Algebra.
  • BOOST version (1.50.0,1.56,1.57.0,1.62.0-cxx11,...) — Boost provides free peer-reviewed portable C++ source libraries.
  • CBLOSC version (1.7.1) — A blocking, shuffling and loss-less compression library
  • EIGEN version (3.2.10) — Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • FFTW version (3.3.4-gromacs,3.3.4) — FFTW is a library for fast fourier transforms. FFTW 3.3.4 library compiled for general use.
  • GEOS version (3.4.2) — GEOS (Geometry Engine - Open Source) is an API for processing spatial geometry.
  • GMP version (6.0.0) — Gnu Multi Precision Libraries
  • GSL version (1.16,2.3) — The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers.
  • IPOPT version (3.12.6) — Ipopt (Interior Point OPTimizert) is a software package for large-scale nonlinear optimization
  • LAPACK version (3.5.0,3.6.1) — LAPACK (Linear Algebra Package) is a standard software library for numerical linear algebra.
  • MIXMODLIB version (3.1) — Mixmod statistical libraries
  • MPC version (1.0.3) — Gnu Mpc is a C library for arithmatics with arbitrarily high precision of complex numbers.
  • MPFR version (3.1.3) — MPFR library is a C library for multiple-precision floating-point computations.
  • NCO version (4.3.0) — The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats.
  • NETCDF version (4.2.0) — NetCDF is a set of software libraries supporting array-oriented scientific data.
  • PARI version (2.7.5) — PARI is a widely used computer algebra system designed for fast computations in number theory
  • SAGA version (2.2.0) — SAGA is a GIS application
  • SDPA version (7.3.8) — SDPA (Semi Definite Programming Algorithm) is one of the efficient software package for solving SDPs.
  • SPARSE version (-) — Sparse works with Python 2.7 and offers a set of packages to deal with sparse matrices
  • SPARSESUITE version (4.2.1) — SuiteSparse is a suite of sparse matrix algorithms.
  • SUNDIALS version (2.5) — SUNDIALS (SUite of Nonlinear and DIfferential/ALgebraic equation Solvers)

Software Libraries, Languages, and Tools

  • ALL-PKGS version (-) — all-pkgs loads Python with a set of popular packages for scientific computing (Numpy, matplotlib, Scipy, pandas, nltk)
  • ANT version (1.9.4) — Ant is a Java library and command-line tool is to drive processes described in build files.
  • APR version (1.5.1) — The Apache Portable Runtime (APR) libraries provide a interface to platform-specific implementations.
  • APRUTIL version (1.5.3) — APR Util provides cross platform libraries for handling OS related operations.
  • BBFTP version (3.2.1) — BBFTP is a file transfer software.
  • BINUTILS version (2.26) — GNU Binutils are a collection of binary tools that do low level operations on binaries.
  • BOTO version (-) — Boto is a Python package that provides interfaces to Amazon Web Services.
  • BZIP2 version (1.0.6) — bzip2 is a freely available, patent free, high-quality data compressor.
  • CANOPY version (1.4.1) — Canopy is the next generation of the Enthought Python Distribution (EPD)
  • CCTOOLS version (4.4.2,5.2.3,5.4.7,6.0.7) — Cooperative Computing Lab is software designed to easily harness large scale distributed systems such as clusters, clouds, and grids.
  • CFITSIO version (3.37) — CFITSIO is a library of C and Fortran subroutines for reading and writing data files in F ITS (Flexible Image Transport System) data format.
  • CIRCOS version (0.68) — Circos is a software package for visualizing data and information in a circular layout.
  • CMAKE version (3.0.1,3.4.1,3.8.0) — CMake is a cross platform make utility
  • CONNECT-CLIENT version (0.2.1,0.3.0,...) — connect-client is command line tool to use OSG from your local machine.
  • CPAN version (perl-5.10) — The Comprehensive Perl Archive Network (CPAN) is a repository for Perl programming language
  • CURL version (7.37.1) — Curl is a command line HTTP client
  • DAKOTA version (6.4.0) — The Dakota toolkit provides a flexible, extensible interface between analysis codes and iterative systems analysis methods.
  • DENDROPY version (-) — DendroPy is a Python library for phylogenetic computing
  • DMTCP version (2.5.0) — DMTCP (Distributed MultiThreaded Checkpointing) transparently checkpoints a single-host or distributed computation in user-space
  • ECTOOLS version (-) — Ectools is a set of tools for correcting long read assembly data
  • EXPAT version (2.1.0) — Expat is an XML parser library written in C.
  • FFMPEG version (0.10.15,2.5.2) — ffmpeg is a complete
  • FPC version (2.6.4) — Free pascal Free Pascal is a 32
  • FREETYPE version (2.5.5) — FreeType 2 provides a simple and easy-to-use API to access font content in a uniform way
  • GCC version (4.6.2,4.6.4,4.8.1,4.9.2,4.9.3,6.2.0) — GCC is a set of compilers for c
  • GD version (2.1.1) — GD is an open source code library for the dynamic creation of images by programmers.
  • GFAL version (7.20) — GFAL2 is a set of file access utilities.
  • GIT version (1.9.0) — Git is a software change management tool.
  • GLOBUS-CLI version (-) — globus-cli is a free command line tool that provides an interface to Globus services
  • GNOME_LIBS version (1.0) — GNOME desktop libraries.
  • HDF5 version (1.8.5-cxx11,1.8.9,1.8.12-cxx11,1.8.12,...) — HDF5 is a library for storing and managing data in flexible
  • IRODS version (4.2.2) — The Integrated Rule-Oriented Data System (iRODS) is open source data management software.
  • JASPER version (1.900.1) — reference implementation of the codec specified in the JPEG
  • JAVA version (7u71,8u25,8u131) — Java
  • JPEG version (6b,9a) — Libjpeg is a widely used C library for reading and writing jpeg image files.
  • LIBGFORTRAN version (4.4.7) —
  • LIBICU version (4.2.1) — International Components for Unicode (ICU) libraries.
  • LIBTIFF version (4.0.4) —
  • LIBXPM version (3.5.10) — LibXPM is a package with X.Org, X11, and libXpm runtime libraries
  • LLVM version (3.6,3.7,3.8.0,5.0.0) — LLVM is a toolkit for the construction of highly optimized compilers, optimizers, and runtime environments.
  • MERCURIAL version (1.9.1) — Mercurial is a source code management tool.
  • MONO version (4.2.1) — Mono is a software platform designed to allow developers to easily create cross platform applications.
  • MPLAYER version (1.1) — Mplayer is an image viewer and editor.
  • MYSQL version (5.1.73) — mysql client tool that provides command line interface to the mysql database.
  • OPENCV version (2.4.10) — OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
  • OPENSIM version (3.3) — OpenSim is an open source software system for biomechanical modeling, simulation and analysis.
  • PAPI version (5.3.2) — PAPI is a performance profiler.
  • PARSL version (-) — Parsl is a parallel scripting library that enables easy parallelism and workflow design.
  • PBSUITE_PKGS version (-) — PBSuite loads python and adds numpy, h5py, and pysam packages.
  • PCRE version (8.35) — PCRE is perl compatible regular expression library.
  • PEGASUS version (4.4.2-image_tools,4.5.3,4.6.0dev,...) — Pegasus is a workflow management system to automate, recover, and debug scientific computations.
  • POPPLER version (0.24.1,0.32) — Poppler is a PDF rendering library based on the xpdf-3.0 code base
  • POVRAY version (3.7) — The Persistence of Vision Raytracer is a high-quality, Free Software tool for creating stunning three-dimensional graphics.
  • PROJ version (4.9.1) — Cartographic projection library
  • PROOT version (2014) — PRoot is a user-space implementation of chroot
  • PROTOBUF version (2.5) — Protocol buffers are Google's language-neutral, platform-neutral, extensible mechanism for serializing structured data – think XML, but smaller, faster, and simpler.
  • PYTHON version (2.7,3.4,3.5.2) — Python is a programming language that lets you work quickly and integrate systems more effectively.
  • RUBY version (2.1) — Ruby is a dynamic
  • RUCIO version (1.6.6) — Distributed Data Management (DDM) system services
  • S3CMD version (-) — S3cmd is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud stora ge service providers that use the S3 protocol
  • SCONS version (2.3.4) — SCons is a software construction tool and is a superior alternative to the classic "Make" build tool.
  • SERF version (1.37) — Serf is a library that provides high performance http client functions.
  • SETTARG version (5.6.2) — The settarg module dynamically and automatically updates "$TARG" and a host of other environment variables.
  • SNAPPY version (1.1.3) — Snappy is a compression and decompression library.
  • STASHCP version (2.6,4.3.0,4.3.1) — Stashcp is a front-end to XRootD caching for OSG Connect Stash.
  • SUBVERSION version (1.8.10) — Subversion is a source control revision tool.
  • SWIFT version (0.94.1,0.96.2) — Swift is a parallel scripting language.
  • TCL version (8.6.2) — Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language.
  • TCSH version (6.20.00) — tcsh is a Unix shell based on and compatible with the C shell (csh). It is essentially the C shell with programmable command-line completion, command-line editing, and a few other features.
  • UNIXODBC version (2.3.2) — The unixODBC Project goals are to develop and promote unixODBC to be the definitive standard for ODBC on non MS Windows platforms.
  • VALGRIND version (3.10) — Valgrind can detect memory management and threading bugs
  • WGET version (1.15) — Wget is a command line HTTP client
  • WXGTK version (3.0.2) — wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, and Linux.
  • XROOTD version (4.1.1,4.2.1) — The XROOTD project aims at giving high performance, scalable fault tolerant access to data repositories of many kinds.
  • XZ version (5.2.2) — XZ Utils is free general-purpose data compression software with a high compression ratio.
  • ZLIB version (1.2.8) — Zlib is a library that provides functions for compression and decompression of data