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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.
  • 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)
  • LAMMPS version (2.0,15May15) — LAMMPS is a particle simulator code.
  • MADGRAPH version (2.1.2,2.2.2) — MadGraph is a monte carlo generator for particle physics interactions
  • OCTAVE version (3.8.1) — Octave is a high-level interpreted language
  • 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.
  • 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.
  • 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.
  • PHENIX version (1.10) — software suite for the determination of molecular structures from X-Ray and other methods.
  • PSI4 version (0.3.74) — 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.
  • 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

Bioinformatics

  • 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
  • HMMER version (3.1) — HMMER searches and aligns homologs of protein sequences using hidden Markov models.
  • MRBAYES version (3.2.2) — MrBayes is a program for Bayesian inference of phylogenetic and evolutionary models.
  • MUSCLE version (3.8.31) — MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation
  • PBSUITE version (14.9.9) — PBSuite is a software for long-read sequencing data from PacBio.
  • SAMTOOLS version (0.1.17,1.3.1) — Samtools is a set of utilities for working with data in sequence alignment map format.
  • 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
  • TOPHAT version (2.0.13,2.1.1) — TopHat is a fast splice junction mapper for RNA-Seq reads.
  • UCLUST version (2.22) — Uclust offers search and clustering algorithms that are often orders of magnitude faster than BLAST.

Numerical Libraries

  • BOOST version (1.50.0,1.56,1.57.0,1.62.0-cxx11,...) — Boost provides free peer-reviewed portable C++ source libraries.
  • 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.
  • 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.
  • 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.
  • 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

  • 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.
  • 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.
  • CMAKE version (3.0.1,3.4.1,3.8.0) — CMake is a cross platform make utility
  • CURL version (7.37.1) — Curl is a command line HTTP client
  • 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
  • GIT version (1.9.0) — Git is a software change management tool.
  • HDF5 version (1.8.9,1.8.12-cxx11,1.8.12,1.8.13-cxx11,...) — HDF5 is a library for storing and managing data in flexible
  • JASPER version (1.900.1) — reference implementation of the codec specified in the JPEG
  • JAVA version (7u71,8u25) — Java
  • JPEG version (6b,9a) — Libjpeg is a widely used C library for reading and writing jpeg image files.
  • LIBGFORTRAN version (4.4.7) —
  • LIBTIFF version (4.0.4) —
  • MERCURIAL version (1.9.1) — Mercurial is a source code management tool.
  • MPLAYER version (1.1) — Mplayer is an image viewer and editor.
  • OPENCV version (2.4.10) — OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library.
  • PAPI version (5.3.2) — PAPI is a performance profiler.
  • PCRE version (8.35) — PCRE is perl compatible regular expression library.
  • POPPLER version (0.24.1,0.32) — Poppler is a PDF rendering library based on the xpdf-3.0 code base
  • PROJ version (4.9.1) — Cartographic projection library
  • PROOT version (2014) — PRoot is a user-space implementation of chroot
  • RUBY version (2.1) — Ruby is a dynamic
  • 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.
  • STASHCP version (2.2,2.5,2.6,3.0,3.1,...) — 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.
  • VALGRIND version (3.10) — Valgrind can detect memory management and threading bugs
  • WGET version (1.15) — Wget is a command line HTTP client