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