software Link description abaqus 6.14.2 http://abaqus.software Abaqus is a software suite for finite .polimi.it/v6.14/index. element analysis and computer-aided html engineering. afni 16.0.00 https://afni.nimh.nih. Analysis of Functional NeuroImages gov/afni/ (AFNI) amber 14.0 http://ambermd.org/ Amber is the collective name for a suite of programs that allow users to carry out molecular dynamics simulations ansys 16.1 http://www.ansys.com The Ansys software suite provides / engineering simulation software for structural mechanics, fluid dynamics, electromagnetics, as well as pre- and post-processing. atlas http://math- Automatically Tuned Linear Algebra atlas.sourceforge.net/ Software avizo 8.1.1 http://www.fei.com/so Avizo is a 3D analysis software for ftware/avizo3d/ scientific and industrial data. Contains Avizo Fire, Avizo Earth, Avizo Green, Avizo Wind bamtools 2.3.0 A programmer's API and an end-user's toolkit for handling BAM files. bedtools 22.19.1 http://bedtools.readth Tools for analyzing genomic features edocs.org/en/latest/ binutils https://www.gnu.org/s A GNU collection of binary utilities such oftware/binutils/ as ld, gprof, as, etc. blas http://www.netlib.org/ The Basic Linear Algebra Subprograms blas/ library blender 276b http://www.blenderna Blender is an open source 3D creation suite. tion.com/ boost http://www.boost.org/ The free peer-reviewed portable C++ source libraries bowtie http://bowtie- A tool for aligning sequencing reads to bio.sourceforge.net/bo long reference sequences wtie2/index.shtml bwa http://bio- The Burrows-Wheeler Alignment tool is bwa.sourceforge.net/ a tool for aligning sequencing against a large reference genome campari2 http://campari.sourcef Campari v2 orge.net/ cblas350 http://www.netlib.org/ CBLAS is BLAS implementation in C blas/#_cblas charm++661 http://charmplusplus. Charm++ is a machine independent org/ parallel programming system. Programs written using this system will run unchanged on MIMD machines with or without a shared memory cmake https://cmake.org/ CMake is a family of tools designed to build, test and package software. CmdStan 250 http://mc- Shell interface to Stan stan.org/interfaces/cm dstan comsol 5.1 https://www.comsol.c COMSOL Multiphysics® is a general- om/release/5.1 purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. cplex 12.6.1 http://www- The IBM ILOG CPLEX Optimization 01.ibm.com/software/ Studio consists of the CPLEX Optimizer commerce/optimizatio for mathematical programming, the IBM n/cplex-optimizer/ ILOG CPLEX CP Optimizer for constraint programming, the Optimization Programming Language (OPL), and an integrated IDE. cube CUBE Uniform Behavioral Encoding generic presentation component cube432 no description given cuda 7 https://developer.nvid CUDA ia.com/cuda- downloads cufflinks 2.2.1 http://cole-trapnell- Cufflinks assembles transcripts, lab.github.io/cufflinks/ estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. ddd 3312 https://www.gnu.org/s GUI to gdb oftware/ddd/ ddt 5.0 http://www.allinea.co Parallel debugger supporting a wide m/products/ddt range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP. ddt 5.1 no description given ddt6.0 Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP dealii821 https://www.dealii.org an open source finite element library / dl_poly405 http://www.ccp5.ac.uk DL_POLY is a parallel molecular /DL_POLY_CLASSIC/ dynamics simulation package doris402 http://doris.tudelft.nl/ Doris stands for delft object-oriented radar interferometric software doxygen1891 http://www.stack.nl/~ Generate documentation from source dimitri/doxygen/index code .html eigen 3.2.0 http://eigen.tuxfamily. Eigen is a C++ template library for linear org/index.php?title=M algebra: matrices, vectors, numerical ain_Page solvers, and related algorithms env2110 no description given espresso511 http://www.quantum- Quantum Espresso is a software suite for espresso.org/ ab initio quantum chemistry methods of electronic-structure calculation and materials modeling eXpress 1.5.1 eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences expresso A lightweight, fast, test-driven development (TDD) framework for Node.js fastqc0.11.2 http://www.bioinform A quality control tool for high atics.babraham.ac.uk/ throughput sequence data. projects/fastqc/ fastx_toolkit0014 http://hannonlab.cshl. fastx_toolkit edu/fastx_toolkit/inde x.html ffmpeg252 https://ffmpeg.org/ Multimedia framework to decode, encode, transcode, mux, demux, stream, filter video and audio. ffmpeg281 Multimedia framework to decode, encode, transcode, mux, demux, stream, filter video and audio. fftw http://www.fftw.org/ Fast Fourier Transform library fftw2 Fast Fourier Transform library (version 2) fftw334 FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) fftw334_intel2015_op FFTW is a C subroutine library for enmp computing the discrete Fourier transform (DFT) fftw334seq no description given fontconfig www.fontconfig.org/ Fontconfig is a library for configuring and customizing font access freebayes0.9.18 A haplotype-based variant detector fsl5.0.8 http://fsl.fmrib.ox.ac.u FSL is a comprehensive library of k/fsl/fslwiki/FSL analysis tools for FMRI, MRI and DTI brain imaging data. fslint File System "lint" discovery and cleaning utility gams24.4.1 https://www.gams.co The General Algebraic Modeling System m/index.htm (GAMS) is a high-level modeling system for mathematical programming and optimization. gaussian_g03e1 http://www.gaussian.c no description given om/ gaussian_g09d01 no description given gcc https://gcc.gnu.org/ Various compilers (C, C++, Objective-C, Java, ...) gcc492 gcc compiler gcc510 gcc compiler gcc520 gcc compiler gdb https://www.gnu.org/s A GNU source-level debugger for C, C++, oftware/gdb/ Java and other languages gdb781 GDB: The GNU Project Debugger gdbm http://www.gnu.org.ua A GNU set of database routines which /software/gdbm/ use extensible hashin geos342 http://geos.osgeo.org/ GEOS - Geometry Engine doxygen/ getorb232 no description given glibc https://www.gnu.org/s The GNU libc libraries oftware/libc/ glibc2141 The GNU C Library glibc220 The GNU C Library gmp https://gmplib.org/ A GNU arbitrary precision library gmp600 A GNU arbitrary precision library graphviz http://www.graphviz.o Graph Visualization Tools rg/ graphviz2380 Graph Visualization Tools gromacs51 http://www.gromacs.o Molecular dynamics package rg/ gromacs_double51 Molecular dynamics package, double precision gsl http://www.gnu.org/s The GNU Scientific Library for oftware/gsl/ numerical analysis gsl116 GSL - GNU Scientific Library gstat2212015 http://www.gstat.org/ gstat - handles geostatical data gview17 https://www.gview.ca/ no description given wiki/GView/WebHom e h5utils1121 https://www.hdfgroup A set of utilities for visualization and .org/tools5desc.html converstion of HDF5 hdf5 https://www.hdfgroup A general purpose library and file format .org/ for storing scientific data hdf51814 HDF5 is a data model, library, and file format for storing and managing data. hdf51814seq no description given hpcx13336icc no description given hpcx13340gcc no description given htslib1.1 http://www.htslib.org/ An implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. hypre200 http://acts.nersc.gov/h Hypre is a library for solving large, ypre/ sparse linear systems of equations on massively parallel computers. hypre2100b_intel201 Hypre is a library for solving large, 50090 sparse linear systems of equations on massively parallel computers. ilmbase Abstraction/convenience libraries ilmbase220 ILMBase - library on top of which OpenEXR is built InsightToolkit470 http://www.itk.org/In ITK is an open-source software toolkit sight/Doxygen/html/ for performing registration and segmentation. InsightToolkit4.8.0 Insight Segmentation and Registration Toolkit (ITK) Intel2016_1 no description given intel_all Dummy package to install all Intel compiler rpms intel_license2015009 no description given 0 IntelPerformanceCou no description given nterMonitor29 IPM202 no description given isl012 http://isl.gforge.inria.f Integer Set Library r/ JAGS340 http://mcmc- JAGS is Just Another Gibbs Sampler jags.sourceforge.net/ julia034 http://julialang.org/ Julia is a high-level, high-performance dynamic programming language for technical computing knitro9.1.0 https://www.artelys.co KNITRO is an optimization software m/en/home library for finding solutions of both continuous optimization models, as well as discrete optimization models lammps20150210 http://lammps.sandia. LAMMPS Molecular Dynamics gov/ Simulator lapack http://www.netlib.org/ Numerical linear algebra package lapack/ libraries lapack350 LAPACK — Linear Algebra PACKage libgtextutils07 libgtextutils libmatheval https://www.gnu.org/s GNU libmatheval is a library (callable oftware/libmatheval/ from C and Fortran) to parse and evaluate symbolic expressions input as text. limic2056 no description given Mathematica1002 https://www.wolfram. no description given com/mathematica/ Mathematica1020 no description given matlab http://www.mathwork matlab software is used for technical s.com computing. matlabR2014b MATLAB(R) is a high-level language and interactive environment for numerical computation, visualization, and programming. metis510 http://glaros.dtc.umn. Serial Graph Partitioning and Fill- edu/gkhome/metis/m reducing Matrix Ordering etis/overview mpc102 http://www.multipreci GNU MPC is a C library for arithmetic of sion.org/index.php?pr complex number with arbitrary og=mpc precision. mpfr http://www.mpfr.org/ A C library for multiple-precision floating-point computations mpfr312 A C library for multiple-precision floating-point computations mpich2_15 https://www.mpich.or A high-performance implementation of g/ MPI mpich2_15_intel2015. A high-performance implementation of 0090 MPI mpir270 http://mpir.org/ A library for arbitrary precision arithmetic mplayer111 https://mplayerhq.hu/ MPlayer is a movie player design7/news.html mplus731 https://www.statmode Latent variable modeling program with a l.com/index.shtml wide variety of analysis capabilities mvapich2 http://mvapich.cse.ohi OSU MVAPICH2 MPI package o-state.edu/ mvapich221 MVAPICH: MPI over InfiniBand, 10GigE/iWARP and RoCE mvapich221_intel201 MVAPICH: MPI over InfiniBand, 50090 10GigE/iWARP and RoCE mvapich221_pgi154 MVAPICH: MPI over InfiniBand, 10GigE/iWARP and RoCE mxml29 no description given namd210 http://www.ks.uiuc.ed NAMD is a parallel, object-oriented u/Research/namd/ molecular dynamics code designed for high-performance simulation of large biomolecular systems namd211 NAMD 2.11 netcdf http://www.unidata.uc Libraries for the Unidata network ar.edu/software/netcdf Common Data Form / netcdf4331 no description given netcdffortran442 no description given ngs1.0.1 NGS Language Bindings ngspice http://ngspice.sourcef A mixed level/signal circuit simulator orge.net/index.html octave382 https://www.gnu.org/s GNU Octave is a high-level interpreted oftware/octave/ language, primarily intended for numerical computations. OpenBUGS323 http://www.openbugs. OpenBUGS net/w/FrontPage opencv http://opencv.org/ Collection of algorithms for computer vision opencv2410 Open Source Computer Vision Library openexr220 http://www.openexr.c OpenEXR is a high dynamic-range om/ (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications. OpenFOAM http://www.openfoam. The open source CFD toolbox com/ openfoam2.3.1 The open source CFD toolbox openmpi https://www.open- A powerful implementation of mpi.org/ MPI/SHMEM otf2151intel20150090 no description given p4est11 http://www.p4est.org/ Parallel AMR on Forests of Octrees papi541_intel201500 http://icl.cs.utk.edu/p Performance Application Programming 90 api/ Interface parallel20150622 http://www.gnu.org/s GNU parallel oftware/parallel/ parallel_studio_xe_2 no description given 016 parallel_studio_xe_2 no description given 016_license paraview420 http://www.paraview. no description given org/ paraview431 Data analysis and visualization application paraview440 no description given parmetis403 http://glaros.dtc.umn. Parallel Graph Partitioning and Fill- edu/gkhome/metis/pa reducing Matrix Ordering rmetis/overview pcre http://www.pcre.org/ Perl-compatible regular expression library pcre836 PCRE Library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PDT320intel2015009 no description given 0 PerformanceReports5 no description given 1 petsc352 https://www.mcs.anl.g Portable, Extensible Toolkit for Scientific ov/petsc/ Computation pgi157 https://www.pgroup.c Portland Group (PGI) is a premier om/about/ supplier of software compilers and tool for parallel computing, known as PGI products. The Portland Group offers optimizing parallel FORTRAN 2003, C99, and C++ compilers and tools for workstations, servers and clusters running Linux, MacOS, and Windows ploticus242 https://sourceforge.ne no description given t/projects/ploticus/?so urce=navbar python27 https://www.python.or Package that installs python27 g/ python279 no description given python342 no description given QT486 http://www.qt.io/ Qt is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language QT5540 Qt is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language QT5_all Dummy package to install all QT5 RPMs quantumwise2014_2 http://quantumwise.co Simulation software for nanoscience m/ R https://www.r- A language for data analysis and project.org/ graphics R320 no description given rarian https://rarian.freedesk Documentation meta-data library top.org/ raxml7.7.6 http://sco.h- RAxML 7.7.6 its.org/exelixis/web/so ftware/raxml/ rdate Tool for getting the date/time from a remote machine RdRand Library for generating random numbers using the RdRand instruction on Intel CPUs readahead Read a preset list of files into memory readline https://cnswww.cns.c A library for editing typed command wru.edu/php/chet/rea lines dline/rluserman.html regexp Simple regular expressions API relion13 http://www2.mrc- relion - REgularised LIkelihood lmb.cam.ac.uk/relion/i OptimisatioN ndex.php/Main_Page rfkill A tool for enabling and disabling wireless devices rhino https://developer.mozi JavaScript for Java lla.org/en- US/docs/Mozilla/Proje cts/Rhino rhnlib Python libraries for the RHN project rhnsd https://access.redhat.c Red Hat Network query daemon om/documentation/en - US/Red_Hat_Network _Satellite/5.0/html/Re ference_Guide/ch- rhnsd.html roipac301 http://roipac.org/cgi- Software for processing synthetic bin/moin.cgi aperture radar data to produce differential interferograms. root60202 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 rootfiles The basic required files for the root user's directory rpcbind Universal Addresses to RPC Program Number Mapper rpm http://www.rpm.org/ The RPM package management system rpmdevtools RPM Development Tools rpmlint Tool for checking common errors in RPM packages rpmrebuild A tool to build rpm file from rpm database rstudio https://www.rstudio.c RStudio om/ rsync https://rsync.samba.or A program for synchronizing files over a g/ network rsyslog Enhanced system logging and kernel message trapping daemons ruby https://www.ruby- An interpreter of object-oriented lang.org/en/ scripting language rubygems The Ruby standard for packaging ruby libraries samtools http://samtools.source Tools for nucleotide sequence forge.net/ alignments in the SAM format samtools0.1.18 Tools for alignments in the SAM format samtools1.1 Tools for alignments in the SAM format samtools1.2 Tools for alignments in the SAM format sas9.4 http://www.sas.com/e SAS is a software suite for advanced n_us/software/sas9.ht analytics, multivariate analyses, business ml intelligence, data management, and predictive analytics. saslwrapper Ruby and Python wrappers for the cyrus sasl library. scalapack202 http://www.netlib.org/ ScaLAPACK — Scalable Linear Algebra scalapack/ PACKage scalasca222intel2015 no description given 0090 schrodingersuites201 http://www.schroding Schrodinger is a scientific leader in 4 er.com/ computational chemistry, providing software solutions and services for life sciences and materials research scorep142intel201500 no description given 90 slepc353 http://slepc.upv.es/ Scalable Library for Eigenvalue Problem Computations snaphu142 no description given SPM8 http://www.fil.ion.ucl. The Statistical Parametric Mapping ac.uk/spm/ (SPM) software package has been designed for the analysis of brain imaging data sequences. stamps33b1 no description given STAN250 http://mc-stan.org/ Stan is a probabilistic programming language stata14 http://www.stata.com/ Stata is a statistical package for new-in-stata/ managing, analyzing, and graphing data. suitesparse http://faculty.cse.tamu A collection of sparse matrix libraries .edu/davis/suitesparse .html suitesparse442 suitesparse is a collection of libraries for computations involving sparse matrices. sundials250 https://computation.ll SUite of Nonlinear and nl.gov/casc/sundials/ Differential/ALgebraic equation Solvers main.html superlu_mt http://crd- SuperLU is a general purpose library for legacy.lbl.gov/~xiaoye/ the direct solution of large, sparse, SuperLU/ nonsymmetric systems of linear equations on high performance machines swig305 http://www.swig.org/ Generate documentation from source code szip21 no description given tau224 https://www.cs.uorego Tuning and Analysis Utilities n.edu/research/tau/ho me.php tau2241intel2015009 no description given 0 tecplot2015r1ex http://www.tecplot.co Tecplot 360 is a CFD and numerical m/ simulation software package used in post-processing simulation results. tophat22.0.13 TopHat is a fast splice junction mapper for RNA-Seq reads. tophat22.0.14 TopHat is a fast splice junction mapper for RNA-Seq reads. totalview8140 Faster fault isolation, improved memory optimization, and dynamic visualization for your high performance computing apps totalview8.15 Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP. totalview8.15.4 Parallel debugger supporting a wide range of parallel architectures and models, including MPI, UPC, CUDA and OpenMP. triangle16 no description given trilinos11121 Libraries for large-scale, complex multi- physics engineering and scientific problems udunits2 http://www.unidata.uc A library for manipulating units of ar.edu/software/uduni physical quantities ts/ udunits2217 no description given valgrind http://valgrind.org/ Tool for finding memory management bugs in programs valgrind3101 Valgrind is an instrumentation framework for building dynamic analysis tools. vasp541 https://www.vasp.at/ no description given vasp_tst541 no description given vaspview VASP Data Viewer visit291 Data analysis and visualization application vmd192 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. voro++046 http://math.lbl.gov/vo Voro++ is a software library for carrying ro++/ out three-dimensional computations of the Voronoi tessellation. vtk http://www.vtk.org/ The Visualization Toolkit - A high level 3D visualization library VTK610 The Visualization Toolkit xblas10248 http://www.netlib.org/ Extra Precise Basic Linear Algebra xblas/ Subroutines xcrysden1560 http://www.xcrysden.o XCrySDen is a crystalline and molecular rg/ structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated xdrf12 XDRF v1.2 xz http://tukaani.org/xz/ LZMA compression utilities xz520 no description given yaml015 http://yaml.org/ YAML 1.1 parser and emitter written in C zlib http://www.zlib.net/ The zlib compression and decompression library zlib 1.2.8 The zlib compression and decompression library