openblasOpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
tensorflowOpen source software library for numerical computation
theanoOptimizing compiler for evaluating mathematical expressions on CPUs and GPUs
caffe-bvlcFast open framework for deep learning (BVLC upstream)
caffe-ibmFast open framework for deep learning (BVLC upstream) with optimizations made by IBM
digitsDeep Learning GPU Training System
caffe-nvFast open framework for deep learning (NVIDIA's fork)
anaconda2Anaconda 2 python distribution
cudaNVIDIA CUDA Toolkit (C, C++, cuda-gdb, cuda-memcheck, gpu accel)
chainerA flexible framework of neural networks for deep learning
gccGNU Compiler Collection (C, C++, Fortran), GNU Compiler Collection (C, C++, Fortran, Go)
mpichOSU MPI
spectrummpiIBM spectrum MPI for power8
torchTorch 7 | Scientific computing framework for LuaJIT
ncclNVIDIA Collectives Communication Library (NCCL) Runtime
AnacondaAnaconda python distribution
Anaconda2Anaconda python distribution, python version 2.7
Anaconda3Anaconda python distribution, python version 3.5
CGALThe Computational Geometry Algorithms Library is a C++ library that aims to provide easy access to efficient and reliable algorithms in computational geometry.
CLAPACKLAPACK linear algebra routines in C
JAGSJust Another Gibbs Sampler (JAGS)
OpenFOAMOpen source CFD package
RR For Statistical Computing
R-parallelParallel packages for R
ViennaCLSet of header files for GPU support
abaqusAbaqus Research Edition
abinitABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.
allpathslgAssembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
ansysEngineering simulation software
ansysEMElectromagnetics simulation software
apbs-staticAdaptive Poisson Boltzmann Solver
atlasATLAS Tuned Linear Algebra (includes LAPACK)
autodocksuiteAutomated molecule docking tool
automakeautomake tools
bamtoolsBAMTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
bedtoolsBedtools is a fast, flexible toolset for genome arithmetic.
boostBOOST template libraries
boost-mpiBOOST template libraries
bowtieShort read aligner
bowtie2Bowtie 2 Fast and Sensitive Read Alignment
bwaBurrows-Wheeler Aligner
cddlibCDD library for fundamental polyhedral computations
cmakeCross Platform Makefile Generator
coraCORA (CORrelation and Analysis) provides an objective evaluation of time-history signal
cudnncuDNN | GPU-accelerated library for deep neural networks
cufflinksTranscriptome assembly and differential expression analysis for RNA-Seq.
dcwGeography Database
diamondSequence Alignment Tool
discovarnew genome assembler
discovardenovonew genome assembler
ea-utilsEA-utils are command line tools for processing biological sequencing data.
eigenEigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
ensightCSM and CFD Post processing
espressonanoscale material modeling
examlExascale Maximum Likelihood (ExaML)
extraeInstrumentation framework to generate execution traces of the most used parallel runtimes.
fastqcFastQC - A quality control tool for high throughput sequence data.
fftwFastest Fourier Transform in the West
flannFLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces.
flintFast Library for Number Theory
gamit-globkGPS measurement analysis software
gatbGenome Assembly and Analysis Tool Box
gatkThe Genome Analysis Toolkit or GATK is a software package developed to analyze high-throughput sequencing data.
gaussianGaussian 09 provides state-of-the-art capabilities for electronic structure modeling.
gdalGeospatial Data Abstraction Library
gdkNVIDIA GPU Deployment Kit
geosGEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS).
glmOpenGL Mathematics
gmap-gsnapGMAP/GSNAP 2017-01-10
gmsh3D finite element grid generator with a build-in CAD engine and post-processor
gnuplotGNU Plot
graphvizGraphviz is open source graph visualization software.
gshhgGeography Database
gslGNU Scientific Library
guileGNU Ubiquitous Intelligent Language for Extensions
harminvHarminv is a free program (and accompanying library) to solve the problem of harmonic inversion — given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.
hdf5Tool suite for managing very large and complex data collections
hisat2HiSat2 Fast and Sensitive Read Alignment
hmmerSequence Homology Search
hplHigh-Performance Linpack
htkHidden Markov Model Toolkit (HTK)
hypreHypre is a library for solving large, sparse linear systems of equations on massively parallel computers
igvThe Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
intelIntel Compilers (C, C++, Fortran)
iperfiPerf - The ultimate speed test tool for TCP, UDP and SCTP