Modules

This is a list of all software available via the modules system on Midway. Use the command module load <modulename> to load any of these modules in to your environment. See Using software modules on Midway for more information.

3D modeling

Application Midway1 Midway2 Description
ArtiSynth artisynth/2.8, artisynth/2.9 (default), artisynth/3.1, artisynth/svn   3-D biomechanical modeling
Blender blender/2.68 (default) blender/2.78a (default) 3D animation suite
POV-Ray povray/3.6.1 (default)   ray tracing program which generates images from text-based scene

Optimization

Application Midway1 Midway2 Description
gurobi gurobi/6.0 (default)   The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types. See why so many companies are choosing Gurobi for better performance, faster development, and better support.

alignment

Application Midway1 Midway2 Description
muscle muscle/3.8 (default), muscle/3.8.31 muscle/3.8.31 (default)  

assembler

Application Midway1 Midway2 Description
OpenGL Extension Wrangler Library (GLEW) glew/1.7, glew/1.9 (default) glew/1.9, glew/2.0.0 (default) cross-platform C/C++ OpenGL extension loading library
Yasm yasm/1.2 (default), yasm/1.3.0 yasm/1.3.0 (default) x86 assembler

astrophysics

Application Midway1 Midway2 Description
CCfits ccfits/2.4 (default) ccfits/2.5 (default) object oriented interface to the cfitsio library
CFITSIO cfitsio/3 (default), cfitsio/3+intel-12.1, cfitsio/3+intel-15.0 cfitsio/3, cfitsio/3+gcc-6.2 (default) library for reading and writing data files in FITS data format
Fermi Science Tools fermi-fssc/v10r0p5, fermi-fssc/v9r31p1 (default), fermi-fssc/v9r33p0 fermi-fssc/v10r0p5 (default) suite of tools for the analysis of both LAT and GBM data
Ionization FRont Interactive Tool (IFrIT) ifrit/3.4 (default)   3D visualization software focused on cosmological simulations
snid snid/5.0 (default) snid/5.0 (default) Supernova Identification software
yt yt/3.0 (default), yt/3.1 yt/3.3 (default) visualization and analysis tool for cosmological data

biology

Application Midway1 Midway2 Description
PhyML PhyML/3.1 (default)   phylogeny software based on the maximum-likelihood principle
AFNI afni/latest (default) afni/latest (default) neuroimaging data analysis
ArtiSynth artisynth/2.8, artisynth/2.9 (default), artisynth/3.1, artisynth/svn   3-D biomechanical modeling
bcftools bcftools/1.3 (default)   a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF
BEAGLE beagle/trunk (default) beagle/trunk (default) library for core calculations with phylogenetics packages
BEAST beast/1.7 (default), beast/1.8, beast/2.3 beast/1.8 (default) Bayesian analysis of molecular sequences
Basic Local Alignment Search Tool (BLAST) blastplus/2.2 (default) blastplus/2.5 (default) biological search alignment tool
bowtie   bowtie/1.1.2 (default) DNA sequence alignment software
bowtie2 bowtie2/2.2.9 (default) bowtie2/2.2.9 (default) DNA sequence alignment software
Bwakit bwa/0.7.10 (default)   Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
cufflinks cufflinks/2.2 (default) cufflinks/2.2 (default) Transcriptome assembly and differential expression analysis for RNA-Seq.
ExaBays exabayes/1.3 (default)   Bayesian tree inference
ExaML examl/git (default)   MPI code for phylogenetic inference using Maximum Likelihood
fastqc fastqc/0.11 (default) fastqc/0.11.5 (default) A quality control tool for high throughput sequence data.
fasttree fasttree/2.1.8 (default) fasttree/2.1.8 (default) FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
fastx_toolkit fastx_toolkit/0.0 (default) fastx_toolkit/0.0 (default) A collection of command-line tools for FASTA sequence files preprocessing
FreeSurfer freesurfer/5.3 (default) freesurfer/5.3, freesurfer/6.0 (default) analysis and visualization of structural and functional brain imaging data
MM/PBSA method for GROMACS g_mmpbsa/1.0.0 (default)   calculation of components of binding energy using MM-PBSA method
Gromacs gromacs/4.5.5, gromacs/4.6+intel-12.1 (default), gromacs/4.6-cuda+intel-12.1, gromacs/5.0+intelmpi-5.0+intel-15.0, gromacs/5.0-cuda+intelmpi-5.0+intel-15.0   molecular dynamics simulation
hmmer hmmer/3.1b2 (default) hmmer/3.1b2 (default) HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
HOOMD-blue hoomd/0.11 (default), hoomd/0.11.0, hoomd/1.0, hoomd/1.1, hoomd/1.1-double, hoomd/1.1-double+intelmpi-5.0+intel-15.0   general-purpose particle simulation toolkit
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) lammps/10Aug2015+intelmpi-5.0+intel-15.0, lammps/9Dec2014+intelmpi-5.0+intel-15.0, lammps/cuda-9Dec2014+intelmpi-5.0+intel-15.0, lammps/trunk (default) lammps/17Nov2016+intelmpi-5.1+intel-16.0 (default) molecular dynamics simulation
Libint libint/1.1 (default), libint/2.0 libint/1.1, libint/2.0 (default), libint/2.3 evaluation of two-body molecular integrals over Gaussian functions and optimizing compiler
mafft mafft/7.310 (default) mafft/7.310 (default) Multiple alignment program for amino acid or nucleotide sequences
mfold mfold/3.6 (default)   RNA structure prediction software
Migrate-n migrate-n/3.6 (default)   estimation of population size and gene flow
mothur mothur/1.36 (default) mothur/1.36 (default) Bioinformatics tool for microbial ecology community
motioncor2   motioncor2/latest (default) This program corrects anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images.
motioncorr motioncorr/2.1 (default) motioncorr/2.1 (default) This program corrects whole frame image motion recordded with dose fractionated image stack.
mpiBLAST mpiblast/trunk (default)   improved implementation of NCBI BLAST, find homology in biological sequences
MrBayes mrbayes/release (default)   Bayesian inference and model choice for phylogenetic and evolutionary models
muscle muscle/3.8 (default), muscle/3.8.31 muscle/3.8.31 (default)  
NAMD namd/2.10+intelmpi-5.0+intel-15.0, namd/2.10-cuda+intelmpi-5.0+intel-15.0, namd/2.10b1, namd/2.12+intelmpi-5.1+intel-16.0, namd/2.9 (default), namd/2.9-cuda namd/2.11+intelmpi-5.1+intel-16.0 (default), namd/2.12+intelmpi-5.1+intel-16.0 parallel molecular dynamics code for biomolecular system simulation
openbabel openbabel/2.3 (default), openbabel/2.3.1   toolbox for using chemical data
picard picard/1.138 (default)   a set of tools in Java for working with sequencing data in the BAM format
PICRUSt picrust/1.0 (default)   bioinformatics software package designed to predict metagenome functional content
prodigal prodigal/2.6.2 (default)   microbial (bacterial and archaeal) gene finding program
pycelegans pycelegans/0.4, pycelegans/0.5, pycelegans/0.61 (default)   Parallel image processing code that identifies C. elegans in images
QIIME qiime/1.6, qiime/1.7 (default), qiime/1.8, qiime/1.9   open source software package for comparison and analysis of microbial communities
RAPSearch rapsearch/2 (default)   Reduced Alphabet based Protein similarity Search
Randomized Axelerated Maximum Likelihood (RAxML) raxml/trunk (default)   sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
samtools samtools/1.2 (default)   suite of programs for interacting with high-throughout sequencing data
tophat tophat/2.0 (default), tophat/2.1   splice junction mapper for RNA-Seq reads
treePL treepl/git (default) treepl/git (default) phylogenetic penalized likelihood program
vmd vmd/1.9, vmd/1.9.1, vmd/1.9.2 (default) vmd/1.9.2 (default) molecular visualization program

browser

Application Midway1 Midway2 Description
firefox firefox/esr (default) firefox/esr (default) web browser

checkpointing

Application Midway1 Midway2 Description
dmtcp dmtcp/2.5 (default) dmtcp/2.5 (default) Distributed MultiThreaded CheckPointing

chemistry

Application Midway1 Midway2 Description
PSI4 Psi4/1.1+intel-16.0 (default)   suite of ab initio quantum chemistry programs
abinit abinit/7.10 (default)   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.
Adaptive Poisson-Boltzmann Software (APBS) apbs/1.3, apbs/1.4 (default)   analysis of solvation properties of molecules
BerkeleyGW berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default) berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0, berkeleygw/1.2.0+openmpi-2.0.1 software package for the evaluation of quasiparticle properties and optical responses of materials and molecules
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
CPMD cpmd/3.15 (default), cpmd/3.17+intelmpi-5.0+intel-15.0 cpmd/3.15+intelmpi-4.0+intel-12.1 (default) parallelized plane wave/pseudopotential implementation of Density Functional Theory
ecce-builder ecce-builder/7 (default)   The Builder enables you to build, visualize, modify, and manipulate 3D images of chemical systems to be used in ECCE calculations.
Quantum ESPRESSO espresso/5.1+intel-12.1, espresso/5.1.1+openmpi-1.8+intel-15.0, espresso/5.3.0+intelmpi-5.0+intel-15.0 (default), espresso/5.3.0-west-1.0.2+intelmpi-5.0+intel-15.0, espresso/5.4.0-epw+intelmpi-5.0+intel-15.0, espresso/5.4.0-west-1.1.0+intelmpi-5.0+intel-15.0, espresso/6.0-epw-4.1+intelmpi-5.1+intel-16.0, espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0 espresso/6.0+intelmpi-5.1+intel-16.0 (default), espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0 suite of codes for electronic-structure calculations and nanoscale materials modeling
MM/PBSA method for GROMACS g_mmpbsa/1.0.0 (default)   calculation of components of binding energy using MM-PBSA method
General Atomic and Molecular Electronic Structure System (GAMESS) gamess/1May2012R1 (default)   molecular quantum chemistry computation
Gaussian gaussian/09RevA.02 (default), gaussian/09RevB.01, gaussian/09RevD.01 gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01 electronic structure and quantum chemistry
gpaw gpaw/0.10+intelmpi-5.0+intel-15.0 (default)   Density-functional theory python code
Gromacs gromacs/4.5.5, gromacs/4.6+intel-12.1 (default), gromacs/4.6-cuda+intel-12.1, gromacs/5.0+intelmpi-5.0+intel-15.0, gromacs/5.0-cuda+intelmpi-5.0+intel-15.0   molecular dynamics simulation
Gromacs compiled with PLUMED gromacs-plumed/1.3+intelmpi-4.0+intel-12.1 (default), gromacs-plumed/1.3+openmpi-1.6   gromacs molecular dynamics simulation compiled with plumed free energy calculation
HOOMD-blue hoomd/0.11 (default), hoomd/0.11.0, hoomd/1.0, hoomd/1.1, hoomd/1.1-double, hoomd/1.1-double+intelmpi-5.0+intel-15.0   general-purpose particle simulation toolkit
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) lammps/10Aug2015+intelmpi-5.0+intel-15.0, lammps/9Dec2014+intelmpi-5.0+intel-15.0, lammps/cuda-9Dec2014+intelmpi-5.0+intel-15.0, lammps/trunk (default) lammps/17Nov2016+intelmpi-5.1+intel-16.0 (default) molecular dynamics simulation
Libint libint/1.1 (default), libint/2.0 libint/1.1, libint/2.0 (default), libint/2.3 evaluation of two-body molecular integrals over Gaussian functions and optimizing compiler
NAMD namd/2.10+intelmpi-5.0+intel-15.0, namd/2.10-cuda+intelmpi-5.0+intel-15.0, namd/2.10b1, namd/2.12+intelmpi-5.1+intel-16.0, namd/2.9 (default), namd/2.9-cuda namd/2.11+intelmpi-5.1+intel-16.0 (default), namd/2.12+intelmpi-5.1+intel-16.0 parallel molecular dynamics code for biomolecular system simulation
NWChem nwchem/6.5+intelmpi-5.0+intel-15.0 (default) nwchem/6.6+intelmpi-5.1+intel-16.0 (default) Software toolkit for computational chemistry
openbabel openbabel/2.3 (default), openbabel/2.3.1   toolbox for using chemical data
OpenFOAM openfoam/2.1 (default), openfoam/pegged+openmpi-1.6   C++ toolbox for developing customized numerical solvers, and pre-/post-processing utilities for solving continuum mechanics problems
OpenMM openmm/5.2, openmm/6.0 (default), openmm/6.1, openmm/6.2   A toolkit for molecular simulation using high performance GPU code.
ORCA orca/3.0 (default)   a general purpose tool for quantum chemistry with emphasis on spectroscopic properties of open-shell molecules
PLUMED plumed/2.1 (default), plumed/2.1+intelmpi-5.0+gcc-4.8, plumed/2.1+intelmpi-5.0+intel-15.0, plumed/2.1+intelmpi-5.1+intel-16.0, plumed/2.2+intelmpi-5.0+intel-15.0   library for free energy calculations in molecular systems
PSI4 psi/4.0+intel-15.0 (default)   suite of ab initio quantum chemistry programs
pyscf   pyscf/1.2.1 (default) Python Module for Quantum Chemistry
siesta siesta/3.2 (default), siesta/trunk-462   SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
wannier90 wannier90/2.0 (default)   Maximally localized Wannier functions.
xc xc/2.2+intel-15.0 (default)   C library for density-functional theory
xcrysden xcrysden/1.5 (default) xcrysden/1.5 (default) XCrySDen is a crystalline and molecular structure visualization program

climate

Application Midway1 Midway2 Description
afterburner afterburner/4.7 (default) afterburner/4.7 (default) The standard post-processor for ECHAM model data.
Climate Data Operators (CDO) cdo/1.5 (default), cdo/1.6 cdo/1.6, cdo/1.7 (default) analysis of climate and NWP model data
wgrib2 wgrib2/0.1 (default)   read and write grib2 files

compilers

Application Midway1 Midway2 Description
Ant ant/1.8.4 (default), ant/1.9 ant/1.8.4 (default), ant/1.9.7 Java library and command-line tool for building Java applications
clang clang/3.6+gcc-4.8 (default), clang/trunk clang/3.8.0, clang/3.9 (default) C compiler from LLVM project
free pascal freepascal/2.6 (default)   Pascal compiler
GNU Compiler Collection (GCC) gcc/4.7, gcc/4.8 (default), gcc/4.9, gcc/6.1 gcc/4.4.7, gcc/6.1, gcc/6.2 (default) C/C++/Fortran compiler suite
Glasgow Haskell Compiler (GHC) ghc/6.8 (default), ghc/7.4, ghc/7.8   optimizing Haskell compiler
Go go/1.3 (default), go/1.6   programming language
Intel Parallel Studio intel/11.1, intel/12.1 (default), intel/13.1, intel/14.0, intel/15.0, intel/16.0 intel/12.1, intel/15.0, intel/16.0 (default) C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
java java/1.7, java/1.8 (default) java/1.7, java/1.8 (default) programming language
Julia julia/0.3 (default), julia/0.4, julia/0.5+intel-15.0, julia/0.5-bw, julia/0.5-bw+intel-15.0, julia/git   programming language
Libint libint/1.1 (default), libint/2.0 libint/1.1, libint/2.0 (default), libint/2.3 evaluation of two-body molecular integrals over Gaussian functions and optimizing compiler
PGI Compiler Suite pgi/2012 (default), pgi/2013, pgi/2016, pgi/2017   C/C++/Fortran compiler suite
racket racket/5.3 (default) racket/6.7 (default) full-spectrum programming language
Yasm yasm/1.2 (default), yasm/1.3.0 yasm/1.3.0 (default) x86 assembler

computation

Application Midway1 Midway2 Description
GNU Octave octave/3.6 (default) octave/4.0 (default) high-level language for numerical computations

container

Application Midway1 Midway2 Description
singularity singularity/2.0, singularity/2.1.2, singularity/2.2.1 (default) singularity/2.2, singularity/2.2.1 (default) Application container

data

Application Midway1 Midway2 Description
CCfits ccfits/2.4 (default) ccfits/2.5 (default) object oriented interface to the cfitsio library
CFITSIO cfitsio/3 (default), cfitsio/3+intel-12.1, cfitsio/3+intel-15.0 cfitsio/3, cfitsio/3+gcc-6.2 (default) library for reading and writing data files in FITS data format
cnvgrib cnvgrib/1.4 (default)   encoder/decoder for GRIB2 meteorological data
curl curl/7.44 (default) curl/7.50 (default) tool and library for transferring data over the internet
ferret ferret/6.9 (default) ferret/6.9 (default) An interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data set
Globus globus/5.2 (default)   data transfer utility
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
GRIB-API grib_api/1.9 (default) grib_api/1.18 (default) encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages
hdf4 hdf4/4.2 (default)   data model, library, and file format for storing and managing data
HDF5 hdf5/1.10+intelmpi-5.0+intel-15.0, hdf5/1.8 (default), hdf5/1.8.15, hdf5/1.8.15+intel-15.0, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.17+pgi-2016 hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.8.15, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.16+openmpi-1.10+intel-16.0, hdf5/1.8.16+openmpi-2.0+intel-16.0, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0 data model, library, and file format for storing and managing data
HDF5 hdf5_hl/1.8.17+pgi-2016 (default) hdf5_hl/1.8.17 (default), hdf5_hl/1.8.17+intel-16.0 data model, library, and file format for storing and managing data
JasPer jasper/1.900 (default) jasper/1.900 (default) reference implementation of the codec specified in the JPEG-2000 Part-1 standard
LevelDB leveldb/1 (default)   key-value storage library
loaddap loaddap/3.7.2 (default)   The Matlab loaddap Tool provides a way to read any DAP-accessible data into Matlab.
NCAR Command Language (NCL) ncl_ncarg/6.1 (default), ncl_ncarg/6.2, ncl_ncarg/6.3 ncl_ncarg/6.2 (default) interpreted language designed for data analysis and visualization
netCDF Operator (NCO) nco/4.2, nco/4.3 (default), nco/4.4 nco/4.4 (default) command-line programs for manipulation and analysis of netCDF-accessible formatted data
netCDF netcdf/3.6.3, netcdf/3.6.3+intel-12.1, netcdf/4.2 (default), netcdf/4.2+intel-12.1, netcdf/4.2+intel-13.1, netcdf/4.3, netcdf/4.3+intel-15.0, netcdf/4.3+pgi-2016, netcdf/4.4+intel-15.0 netcdf/4.2, netcdf/4.3, netcdf/4.4.1 (default), netcdf/4.4.1+intel-16.0, netcdf/4.4.1.1+intelmpi-5.1+intel-16.0 software library for self-describing, machine-independent data formats
netcdf-cxx   netcdf-cxx/4.2+intelmpi-5.1+intel-16.0 (default) C++ bindings for netcdf
netcdf-fortran netcdf-fortran/4.2+intel-13.1, netcdf-fortran/4.4+intel-15.0 (default), netcdf-fortran/4.4+pgi-2016 netcdf-fortran/4.4.4 (default), netcdf-fortran/4.4.4+intel-16.0, netcdf-fortran/4.4.4+intelmpi-5.1+intel-16.0 Fortran bindings for Netcdf
netcdf-java   netcdf-java/4.6.8+intelmpi-5.1+intel-16.0 (default) NetCDF-Java Library is a Java interface to NetCDF files, as well as to many other types of scientific data formats.
openbabel openbabel/2.3 (default), openbabel/2.3.1   toolbox for using chemical data
panoply panoply/4 (default)   Panoply is a cross-platform application that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets.
Google Protocol Buffers protobuf/2.4, protobuf/2.5 (default) protobuf/2.7 (default) serialize structured data
QD qd/2.3.14 (default)   computational library
redis redis/2.8 (default) redis/3.2 (default) A key-value cache and store server
spark spark/1.3, spark/1.4, spark/1.5, spark/1.6 (default), spark/2.0.2, spark/2.1 spark/2.0.2, spark/2.1 (default) Apache Spark is a fast and general engine for large-scale data processing.
sra_toolkit sra_toolkit/2.6, sra_toolkit/2.8 (default) sra_toolkit/2.6, sra_toolkit/2.8 (default) a collection of tools and libraries for using data in the INSDC Sequence Read Archives
treePL treepl/git (default) treepl/git (default) phylogenetic penalized likelihood program
UnRAR unrar/5.0 (default) unrar/5.4 (default) utility for extracting rar format archives
Xerces-C++ XML Parser xerces/3.1, xerces/3.1.4 (default) xerces/2.8.0, xerces/3.1.4 (default) validating XML parser written in C++
Xerces-C++ XML Parser xercesc/2.8 (default)   validating XML parser written in C++
zlib zlib/1.2 (default) zlib/1.2 (default) compression library

data analysis

Application Midway1 Midway2 Description
ROOT ROOT/5.26, ROOT/5.34 (default), ROOT/5.34+python-2.7-2014q1, ROOT/6.06 ROOT/5.34.14, ROOT/6.06.08 (default) program library for particle physics data analysis
CLUTO cluto/2.1 (default) cluto/2.1 (default) clustering low- and high-dimensional datasets and for analysis of various clusters
hmmer hmmer/3.1b2 (default) hmmer/3.1b2 (default) HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
jags jags/4.0.1 (default), jags/4.2.0 jags/4.2.0 (default) JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
libspatialindex spatialindex/1.8 (default) spatialindex/1.8 (default) library for spatial indexing and queries
sra_toolkit sra_toolkit/2.6, sra_toolkit/2.8 (default) sra_toolkit/2.6, sra_toolkit/2.8 (default) a collection of tools and libraries for using data in the INSDC Sequence Read Archives
Teem teem/trunk (default) teem/trunk (default) scientific raster data visualization
Weka weka/3.6 (default)   machine learning algorithms

database

Application Midway1 Midway2 Description
Basic Local Alignment Search Tool (BLAST) blastplus/2.2 (default) blastplus/2.5 (default) biological search alignment tool
GNU dbm (GDBM) gdbm/1.8 (default)   library for on-disk hashed databases
hdf4 hdf4/4.2 (default)   data model, library, and file format for storing and managing data
HDF5 hdf5/1.10+intelmpi-5.0+intel-15.0, hdf5/1.8 (default), hdf5/1.8.15, hdf5/1.8.15+intel-15.0, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.17+pgi-2016 hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.8.15, hdf5/1.8.16+intelmpi-5.1+intel-16.0, hdf5/1.8.16+openmpi-1.10+intel-16.0, hdf5/1.8.16+openmpi-2.0+intel-16.0, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0 data model, library, and file format for storing and managing data
HDF5 hdf5_hl/1.8.17+pgi-2016 (default) hdf5_hl/1.8.17 (default), hdf5_hl/1.8.17+intel-16.0 data model, library, and file format for storing and managing data
hmmer hmmer/3.1b2 (default) hmmer/3.1b2 (default) HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
LevelDB leveldb/1 (default)   key-value storage library
SpatiaLite libspatialite/4.0 (default) libspatialite/4.3 (default) extension of SQLite core with Spatial SQL capabilities
mpiBLAST mpiblast/trunk (default)   improved implementation of NCBI BLAST, find homology in biological sequences
mysql mysql/5.6 (default)   MySQL database server
netCDF netcdf/3.6.3, netcdf/3.6.3+intel-12.1, netcdf/4.2 (default), netcdf/4.2+intel-12.1, netcdf/4.2+intel-13.1, netcdf/4.3, netcdf/4.3+intel-15.0, netcdf/4.3+pgi-2016, netcdf/4.4+intel-15.0 netcdf/4.2, netcdf/4.3, netcdf/4.4.1 (default), netcdf/4.4.1+intel-16.0, netcdf/4.4.1.1+intelmpi-5.1+intel-16.0 software library for self-describing, machine-independent data formats
PostgreSQL postgresql/9.2 (default), postgresql/9.3, postgresql/9.6 postgresql/9.6 (default) client for postgres database server
redis redis/2.8 (default) redis/3.2 (default) A key-value cache and store server

debugging

Application Midway1 Midway2 Description
Allinea Performance Reports PerformanceReports/7.0 (default) PerformanceReports/7.0 (default) profiler
GNU Data Display Debugger (DDD) ddd/3.3 (default) ddd/3.3+gcc-6.2 (default) graphical front-end for command-line debuggers
Allinea DDT ddt/5.0, ddt/7.0 (default) ddt/5.0, ddt/7.0 (default) debugger
GNU Debugger (GDB) gdb/7.10, gdb/7.9 (default) gdb/7.12+gcc-6.2 (default) A command-line program for tracing and altering the execution of compiled programs for the purposes of debugging.
Valgrind valgrind/3.7, valgrind/3.8, valgrind/3.9 (default) valgrind/3.12+gcc-6.2 (default) debugging and profiling tools, most commonly used to locate memory errors, including leaks, but also can be used to debug threaded codes and profile cache efficiency.
Valkyrie valkyrie/2.0 (default)   GUI for analyzing output from Valgrind tools

development

Application Midway1 Midway2 Description
Anaconda2 Anaconda2/4.1.1 (default) Anaconda2/4.3.0 (default) Anaconda2 python distribution
Anaconda3 Anaconda3/4.1.1 (default) Anaconda3/4.1.1, Anaconda3/4.3.0 (default) Anaconda2 python distribution
Allinea Performance Reports PerformanceReports/7.0 (default) PerformanceReports/7.0 (default) profiler
UCLAPhonotacticLearner UCLAPhonotacticLearner/latest (default) UCLAPhonotacticLearner/latest (default) A Maximum Entropy Model of Phonotactics and Phonotactic Learning
AMD Accelerated Parallel Processing SDK amdappsdk/2.7 (default)   development platform for accelerating applications
Ant ant/1.8.4 (default), ant/1.9 ant/1.8.4 (default), ant/1.9.7 Java library and command-line tool for building Java applications
ANother Tool for Language Recognition (ANTLR) antlr/2.7 (default) antlr/2.7.7 (default) parser generator for computer-based language recognition
Autoconf autoconf/2.68 (default) autoconf/2.68 (default) configures software source code packages
Automake automake/1.13 (default) automake/1.13 (default) automatically generates makefile
Bash Automated Testing System (BATS) bats/latest (default) bats/latest (default) TAP compliant testing framework for bash
Boost boost/1.50, boost/1.51, boost/1.55+python-2.7-2014q1, boost/1.58+intel-15.0, boost/1.58+openmpi-1.8, boost/1.58+python-2.7-2015q2, boost/1.61 (default), boost/1.62.0+gcc-4.7, boost/1.62.0+gcc-6.1, boost/1.62.0+intelmpi-5.1+intel-16.0, boost/1.62.0+openmpi-1.6+gcc-4.7 boost/1.50, boost/1.51.0 (default), boost/1.62.0, boost/1.62.0+intelmpi-5.1+intel-16.0, boost/1.62.0+openmpi-1.6, boost/1.63.0+gcc-6.2 portable C++ source libraries
Caffe caffe/git (default)   framework for deep learning
check   check/0.10.0 (default) Check is a unit testing framework for C
clang clang/3.6+gcc-4.8 (default), clang/trunk clang/3.8.0, clang/3.9 (default) C compiler from LLVM project
cmake cmake/2.8, cmake/3.2, cmake/3.4, cmake/3.6.1 (default) cmake/3.6.2 (default) cross-platform build system
Nvidia CUDA Toolkit cuda/4.2, cuda/5.0, cuda/5.5, cuda/6.5 (default), cuda/7.0, cuda/7.5, cuda/8.0 cuda/6.5 (default), cuda/7.5, cuda/8.0 parallel computing platform and programming model
Nvidia cuDNN cudnn/6.5 (default)   GPU accelerated deep learning
GNU Data Display Debugger (DDD) ddd/3.3 (default) ddd/3.3+gcc-6.2 (default) graphical front-end for command-line debuggers
Allinea DDT ddt/5.0, ddt/7.0 (default) ddt/5.0, ddt/7.0 (default) debugger
dos2unix dos2unix/7.3.5 (default) dos2unix/7.3.5 (default) Dos2Unix / Unix2Dos - Text file format converters
free pascal freepascal/2.6 (default)   Pascal compiler
GNU Compiler Collection (GCC) gcc/4.7, gcc/4.8 (default), gcc/4.9, gcc/6.1 gcc/4.4.7, gcc/6.1, gcc/6.2 (default) C/C++/Fortran compiler suite
gcj   gcj/6.2+gcc-6.2 (default) GNU implementation of java
GNU Debugger (GDB) gdb/7.10, gdb/7.9 (default) gdb/7.12+gcc-6.2 (default) A command-line program for tracing and altering the execution of compiled programs for the purposes of debugging.
Glasgow Haskell Compiler (GHC) ghc/6.8 (default), ghc/7.4, ghc/7.8   optimizing Haskell compiler
git-lfs git-lfs/1.3 (default) git-lfs/1.4 (default) an open source git extension for versioning large files
OpenGL Extension Wrangler Library (GLEW) glew/1.7, glew/1.9 (default) glew/1.9, glew/2.0.0 (default) cross-platform C/C++ OpenGL extension loading library
Google Logging Library (glog) glog/0.3 (default) glog/0.3 (default) application-level logging
Go go/1.3 (default), go/1.6   programming language
GNU Scientific Library (GSL) gsl/1.15, gsl/1.16 (default), gsl/2.2.1+gcc-6.1, gsl/2.2.1+intel-15.0, gsl/2.2.1+intel-16.0 gsl/1.16, gsl/2.2.1 (default), gsl/2.2.1+gcc-6.2, gsl/2.2.1+intel-12.1, gsl/2.2.1+intel-16.0 numerical C/C++ numerical library
haskell-stack haskell-stack/1.1 (default) haskell-stack/1.1 (default) cross-platform program for developing Haskell projects
Intel Parallel Studio intel/11.1, intel/12.1 (default), intel/13.1, intel/14.0, intel/15.0, intel/16.0 intel/12.1, intel/15.0, intel/16.0 (default) C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
Java 3D (j3d) j3d/1.5 (default)   3D API for Java
java java/1.7, java/1.8 (default) java/1.7, java/1.8 (default) programming language
JRuby jruby/1.7 (default)   implementation of Ruby programming language atop the Java Virtual Machine
Julia julia/0.3 (default), julia/0.4, julia/0.5+intel-15.0, julia/0.5-bw, julia/0.5-bw+intel-15.0, julia/git   programming language
libcheck libcheck/0.10 (default)   Unit testing framework for C
libedit   libedit/0.3 (default) Non-GPL replacement for readline library. A spin-off from NetBSD code. Aim is for 100% readline API compatibility
libffi libffi/3.2 (default) libffi/3.2 (default) A portable foreign-function interface library
libgmp libgmp/6.1 (default) libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 The GNU multiple precision arithmetic library
libpng   libpng/1.2 (default) Reference library for supporting the Portable Network Graphics (PNG) format.
GNU Libtool libtool/2.4 (default)   generic library support script
lua   lua/5.3.3 (default) Lua is a powerful, efficient, lightweight, embeddable scripting language
Mathematica mathematica/10.0, mathematica/10.2, mathematica/8.0, mathematica/9.0 (default) mathematica/10.2 (default) symbolic mathematical software
Matlab matlab/2011b, matlab/2012a, matlab/2012b, matlab/2013b, matlab/2014b (default), matlab/2016a, matlab/2016b matlab/2014b (default), matlab/2016a high level language and interactive environment for numerical computation, visualization, and programming
Maven maven/3.1 (default)   software project management and comprehension tool
Metis metis/5.1 (default) metis/5.1 (default) Serial Graph Partitioning and Fill-reducing Matrix Ordering
Mono mono/2.10 (default) mono/2.10 (default) open source implementation of Microsoft’s .NET Framework
Node.js node/0.10.29 (default) node/6.9 (default) framework for building network applications
Program Database Toolkit (PDT) pdtoolkit/3.18 (default)   framework for analyzing source code
php php/7.0 (default) php/7.0 (default) general-purpose scripting language for web development
Python python/2.7, python/2.7-2013q4, python/2.7-2014q1, python/2.7-2014q2, python/2.7-2014q3, python/2.7-2015q1, python/2.7-2015q2 (default), python/2.7.12+gcc-4.7, python/2.7.12+gcc-6.1, python/2.7.12+intel-16.0, python/3.3, python/3.4-2015q1, python/3.5.2+gcc-4.8, python/3.5.2+intel-16.0 python/2.7.12 (default), python/2.7.12+intel-16.0, python/2.7.12-nompi, python/2.7.13+gcc-6.2, python/3.5.2, python/3.5.2+intel-16.0 A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks.
Python   python_ucs4/2.7.12 (default), python_ucs4/2.7.13+gcc-6.2 A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks.
QT qt/3.3, qt/4.7, qt/4.8 (default) qt/4.8, qt/5.7 (default) cross-platform application framework
racket racket/5.3 (default) racket/6.7 (default) full-spectrum programming language
Ruby ruby/2.1 (default) ruby/2.3 (default) programming language
scilab scilab/5.5 (default) scilab/5.5 (default) environment for numerical computation
Apache Serf   serf/1.3.9 (default) High performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library
SML/NJ smlnj/110.74, smlnj/110.76, smlnj/110.79, smlnj/110.80 (default) smlnj/110.79, smlnj/110.80 (default) compiler for the Standard ML ‘97 programming language
Snack snack/2.2 (default)   create audio applications with a scripting language
Google Sparsehash sparsehash/2.0 (default) sparsehash/2.0 (default) hash-map library implementation
Subversion subversion/1.6, subversion/1.7, subversion/1.8 (default), subversion/keyring subversion/1.9.4 (default) version control system
swig swig/3.0 (default)   SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
Valgrind valgrind/3.7, valgrind/3.8, valgrind/3.9 (default) valgrind/3.12+gcc-6.2 (default) debugging and profiling tools, most commonly used to locate memory errors, including leaks, but also can be used to debug threaded codes and profile cache efficiency.
Yasm yasm/1.2 (default), yasm/1.3.0 yasm/1.3.0 (default) x86 assembler

docs

Application Midway1 Midway2 Description
Doxygen doxygen/1.8 (default) doxygen/1.8 (default) documentation generation from annotated sources in various languages such as C, C++, Java, etc
flex flex/2.5 (default) flex/2.6.1 (default), flex/2.6.4 Fast lexical analyzer generator
gettext   gettext/0.19.8 (default) Set of tools that provides a framework to help other GNU packages produce multi-lingual messages
Texinfo texinfo/4.13a (default) texinfo/4.13a, texinfo/6.3 (default) official GNU documentation format

documentation

Application Midway1 Midway2 Description
Doxygen doxygen/1.8 (default) doxygen/1.8 (default) documentation generation from annotated sources in various languages such as C, C++, Java, etc
Texinfo texinfo/4.13a (default) texinfo/4.13a, texinfo/6.3 (default) official GNU documentation format
TeX Live texlive/2012, texlive/2016 (default) texlive/2016, texlive/2017 (default) TeX typesetting system, including extensions (etex, latex, pdflatex, etc.)

electronic structure

Application Midway1 Midway2 Description
pyscf   pyscf/1.2.1 (default) Python Module for Quantum Chemistry

fluid dynamics

Application Midway1 Midway2 Description
OpenFOAM openfoam/2.1 (default), openfoam/pegged+openmpi-1.6   C++ toolbox for developing customized numerical solvers, and pre-/post-processing utilities for solving continuum mechanics problems

general programming

Application Midway1 Midway2 Description
R R/2.15, R/2.15+intel-12.1, R/3.0, R/3.0+intel-12.1, R/3.1, R/3.1+intel-15.0, R/3.2 (default), R/3.2+intel-15.0, R/3.3.2 R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4 (default) programming language/environment for statistical computation and graphics
Go go/1.3 (default), go/1.6   programming language
haskell-stack haskell-stack/1.1 (default) haskell-stack/1.1 (default) cross-platform program for developing Haskell projects
IDL idl/8.2 (default) idl/8.2 (default) scientific programming language for visualization
java java/1.7, java/1.8 (default) java/1.7, java/1.8 (default) programming language
JRuby jruby/1.7 (default)   implementation of Ruby programming language atop the Java Virtual Machine
libffi libffi/3.2 (default) libffi/3.2 (default) A portable foreign-function interface library
libgmp libgmp/6.1 (default) libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 The GNU multiple precision arithmetic library
libpng   libpng/1.2 (default) Reference library for supporting the Portable Network Graphics (PNG) format.
Matlab matlab/2011b, matlab/2012a, matlab/2012b, matlab/2013b, matlab/2014b (default), matlab/2016a, matlab/2016b matlab/2014b (default), matlab/2016a high level language and interactive environment for numerical computation, visualization, and programming
Node.js node/0.10.29 (default) node/6.9 (default) framework for building network applications
numba numba/0.20+python-2.7-2015q2 (default)   Python JIT compilation layer for numeric codes
GNU Octave octave/3.6 (default) octave/4.0 (default) high-level language for numerical computations
Perl perl/5.18 (default) perl/5.24.1 (default) programming language
php php/7.0 (default) php/7.0 (default) general-purpose scripting language for web development
PyPy pypy/1.8 (default)   fast Python implementation
Python python/2.7, python/2.7-2013q4, python/2.7-2014q1, python/2.7-2014q2, python/2.7-2014q3, python/2.7-2015q1, python/2.7-2015q2 (default), python/2.7.12+gcc-4.7, python/2.7.12+gcc-6.1, python/2.7.12+intel-16.0, python/3.3, python/3.4-2015q1, python/3.5.2+gcc-4.8, python/3.5.2+intel-16.0 python/2.7.12 (default), python/2.7.12+intel-16.0, python/2.7.12-nompi, python/2.7.13+gcc-6.2, python/3.5.2, python/3.5.2+intel-16.0 A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks.
Python   python_ucs4/2.7.12 (default), python_ucs4/2.7.13+gcc-6.2 A popular high-level, general purpose programming language with a large set of libraries and packages for many scientific and research tasks.
rstudio rstudio/0.97, rstudio/0.98, rstudio/0.99 (default) rstudio/1.1.9 (default) Integrated development environment (IDE) for R.
Ruby ruby/2.1 (default) ruby/2.3 (default) programming language
SML/NJ smlnj/110.74, smlnj/110.76, smlnj/110.79, smlnj/110.80 (default) smlnj/110.79, smlnj/110.80 (default) compiler for the Standard ML ‘97 programming language
Snack snack/2.2 (default)   create audio applications with a scripting language

genetics

Application Midway1 Midway2 Description
admixture admixture/1.3.0 (default)   Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets using the same model as STRUCTURE
bcftools bcftools/1.3 (default)   a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF
bedtools bedtools/2.25 (default) bedtools/2.26 (default) The bedtools utilities are a collection of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
bowtie   bowtie/1.1.2 (default) DNA sequence alignment software
bowtie2 bowtie2/2.2.9 (default) bowtie2/2.2.9 (default) DNA sequence alignment software
cufflinks cufflinks/2.2 (default) cufflinks/2.2 (default) Transcriptome assembly and differential expression analysis for RNA-Seq.
ExaML examl/git (default)   MPI code for phylogenetic inference using Maximum Likelihood
fastqc fastqc/0.11 (default) fastqc/0.11.5 (default) A quality control tool for high throughput sequence data.
fastx_toolkit fastx_toolkit/0.0 (default) fastx_toolkit/0.0 (default) A collection of command-line tools for FASTA sequence files preprocessing
gemma gemma/0.95 (default)   Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS)
HyPhy hyphy/2.2 (default)   software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning
mfold mfold/3.6 (default)   RNA structure prediction software
plink plink/1.07, plink/1.90 (default) plink/1.07, plink/1.90 (default) PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
samtools samtools/1.2 (default)   suite of programs for interacting with high-throughout sequencing data
sickle sickle/1.33 (default) sickle/1.33 (default) A windowed adaptive trimming tool for FASTQ files using quality
tophat tophat/2.0 (default), tophat/2.1   splice junction mapper for RNA-Seq reads
trim_galore trim_galore/0.4 (default)   wrapper to automate trimming of nucleotide sequences
trinity trinity/2.2 (default) trinity/2.2 (default) a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data

genetics and genomics

Application Midway1 Midway2 Description
BEAGLE beagle/trunk (default) beagle/trunk (default) library for core calculations with phylogenetics packages
BEAST beast/1.7 (default), beast/1.8, beast/2.3 beast/1.8 (default) Bayesian analysis of molecular sequences
bedtools bedtools/2.25 (default) bedtools/2.26 (default) The bedtools utilities are a collection of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
Basic Local Alignment Search Tool (BLAST) blastplus/2.2 (default) blastplus/2.5 (default) biological search alignment tool
Bwakit bwa/0.7.10 (default)   Burrow-Wheeler Aligner for pairwise alignment between DNA sequences
ExaBays exabayes/1.3 (default)   Bayesian tree inference
HyPhy hyphy/2.2 (default)   software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning
mpiBLAST mpiblast/trunk (default)   improved implementation of NCBI BLAST, find homology in biological sequences
MrBayes mrbayes/release (default)   Bayesian inference and model choice for phylogenetic and evolutionary models
PICRUSt picrust/1.0 (default)   bioinformatics software package designed to predict metagenome functional content
QIIME qiime/1.6, qiime/1.7 (default), qiime/1.8, qiime/1.9   open source software package for comparison and analysis of microbial communities
Randomized Axelerated Maximum Likelihood (RAxML) raxml/trunk (default)   sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
subread subread/1.5 (default)   Read aligner that maps reads from DNA and RNA sequencing
trinity trinity/2.2 (default) trinity/2.2 (default) a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
UCLUST uclust/1.2.22q (default)   clustering algorithm
vcftools vcftools/0.1 (default) vcftools/0.1 (default) VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

genome

Application Midway1 Midway2 Description
STAR STAR/2.5, STAR/2.5.3a (default), STAR/2.5_static   Spliced Transcripts Alignment to a Reference
plink plink/1.07, plink/1.90 (default) plink/1.07, plink/1.90 (default) PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

genomics

Application Midway1 Midway2 Description
admixture admixture/1.3.0 (default)   Maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets using the same model as STRUCTURE
bedtools bedtools/2.25 (default) bedtools/2.26 (default) The bedtools utilities are a collection of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome.
gemma gemma/0.95 (default)   Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model and some of its close relatives for genome-wide association studies (GWAS)
interproscan interproscan/5 (default) interproscan/5 (default) Software package that allows sequences (protein and nucleic) to be scanned against InterPro’s signatures
plink plink/1.07, plink/1.90 (default) plink/1.07, plink/1.90 (default) PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
redundans redundans/0.13b (default)   Redundans takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly.
spades spades/3.8 (default)   solves important algorithmic and computational problems of contemporary genomics and proteomics

geoscience

Application Midway1 Midway2 Description
Geospatial Data Abstraction Library (GDAL) gdal/1.10 (default), gdal/1.11, gdal/1.11-hdf4, gdal/1.9 gdal/2.1 (default) translator library for raster and vector geospatial data
Geometry Engine - Open Source (GEOS) geos/3.4 (default) geos/3.6 (default) spatial predicates and functions for processing geometry
GrADS grads/1.8, grads/1.9, grads/2.0 (default) grads/2.0 (default) manipulation and visualization of earth science data
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
Parallel Ice Sheet Model (PISM) pism/0.6 (default)   ice sheet model
PROJ.4 proj/4.8 (default), proj/4.9 proj/4.9 (default) cartographic projections library
QGIS qgis/1.8 (default)   geographic information system
UDUNITS udunits/2.1 (default) udunits/2.2 (default) support package for units of physical quantities

graphical interfaces

Application Midway1 Midway2 Description
OpenGL Extension Wrangler Library (GLEW) glew/1.7, glew/1.9 (default) glew/1.9, glew/2.0.0 (default) cross-platform C/C++ OpenGL extension loading library
QT qt/3.3, qt/4.7, qt/4.8 (default) qt/4.8, qt/5.7 (default) cross-platform application framework
Qt Widgets for Technical Applications (QWT) qwt/6.0 (default)   Qt widgets for technical applications
Tcl Library tcllib/1.15 (default) tcllib/1.15, tcllib/1.18 (default) library of standard routines for Tcl
Tk Library tklib/0.5 (default)   utility modules for Tcl
wxWidgets wxwidgets/2.8 (default), wxwidgets/3.0 wxwidgets/3.0.0 (default) cross-platrform GUI library

graphs

Application Midway1 Midway2 Description
mcl mcl/14.137 (default) mcl/14.137 (default) Markov Cluster Algorithm

high energy physics

Application Midway1 Midway2 Description
ROOT ROOT/5.26, ROOT/5.34 (default), ROOT/5.34+python-2.7-2014q1, ROOT/6.06 ROOT/5.34.14, ROOT/6.06.08 (default) program library for particle physics data analysis
CERN Program Library (CERNLIB) cernlib/2006b (default)   collection of software for various needs of a physics research laboratory
Class Library for High Energy Physics (CLHEP) clhep/2.2 (default) clhep/2.3 (default) C++ mathematical library for high energy physics analysis
Fermi Science Tools fermi-fssc/v10r0p5, fermi-fssc/v9r31p1 (default), fermi-fssc/v9r33p0 fermi-fssc/v10r0p5 (default) suite of tools for the analysis of both LAT and GBM data
Geant4 geant4/10.00 (default), geant4/10.01, geant4/10.02+gcc-4.8 geant4/10.01 (default) a toolkit for the simulation of particles through matter

high performance computing

Application Midway1 Midway2 Description
CCTools cctools/3.6 (default)   collection of software for harnessing large scale distributed systems
Connect Client connect-client/0.5.2 (default)   Set of programs and files for linking a campus research computing cluster to a CI Connect instance which uses HTCondor to submit jobs to the Open Science Grid
Intel MPI Library intelmpi/4.0, intelmpi/4.0+intel-12.1 (default), intelmpi/4.1, intelmpi/4.1+intel-12.1, intelmpi/4.1+intel-13.1, intelmpi/4.1+intel-14.0, intelmpi/5.0, intelmpi/5.0+gcc-4.8, intelmpi/5.0+intel-15.0, intelmpi/5.1+intel-16.0 intelmpi/4.0+intel-12.1, intelmpi/5.0+intel-15.0, intelmpi/5.1+intel-16.0 (default) MPI library
MPI for Python (mpi4py) mpi4py/1.3+intelmpi-4.0 (default), mpi4py/1.3+python-2.7-2015q1, mpi4py/1.3+python-2.7-2015q2, mpi4py/1.3+python-3.4-2015q1, mpi4py/1.3-2014q1+intelmpi-4.0, mpi4py/1.3-2014q3+intelmpi-4.0   Python bindings for the Message Passing Interface (MPI) standard
MVAPICH2 mvapich2/1.8+pgi-2012, mvapich2/1.9 (default), mvapich2/1.9+intel-12.1, mvapich2/1.9+pgi-2012, mvapich2/2.0, mvapich2/2.0+intel-12.1, mvapich2/2.0+intel-16.0 mvapich2/2.2 (default) MPI library
OpenMPI openmpi/1.10+pgi-2016, openmpi/1.4.5+intel-11.1, openmpi/1.6 (default), openmpi/1.6+gcc-4.7, openmpi/1.6+intel-12.1, openmpi/1.6+pgi-2012, openmpi/1.8, openmpi/1.8+gcc-4.8, openmpi/1.8+intel-12.1, openmpi/1.8+intel-15.0, openmpi/2.0+intel-16.0, openmpi/2.0.1+gcc-4.7, openmpi/2.0.1+gcc-6.1 openmpi/1.10+intel-16.0, openmpi/1.10+pgi-2016, openmpi/1.6, openmpi/1.6+intel-12.1, openmpi/1.8, openmpi/2.0+intel-16.0, openmpi/2.0.1 (default), openmpi/2.0.2+gcc-6.2 MPI library
Swift swift/0.94.1, swift/0.95 (default), swift/0.96, swift/testing swift/0.95 (default) workflow scripting language
swift-conf swift-conf/1.0 (default)   configuration for swift on Midway

image processing

Application Midway1 Midway2 Description
AFNI afni/latest (default) afni/latest (default) neuroimaging data analysis
Nvidia cuDNN cudnn/6.5 (default)   GPU accelerated deep learning
Diderot diderot/trunk, diderot/vis12 (default)   parallel domain-specific language for image analysis and visualization
eman eman/2.1 (default), eman/2.12, eman/daily   A suite of scientific image processing focusing on single particle reconstruction.
fiji fiji/1.47 (default), fiji/1.49 fiji/0 (default) A distribution of ImageJ with many useful pluging from the community
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
JasPer jasper/1.900 (default) jasper/1.900 (default) reference implementation of the codec specified in the JPEG-2000 Part-1 standard
OpenCV opencv/2.4 (default), opencv/2.4+python-2.7-2015q1, opencv/3.1 opencv/2.4 (default) computer vision and machine learning software library
SPM spm/12, spm/8 (default)   statistical parametric mapping

imaging

Application Midway1 Midway2 Description
dicom3tools dicom3tools/1 (default) dicom3tools/1 (default) command line utilities for creating, modifying, dumping and validating files of DICOM attributes
gate gate/7.1 (default)   Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy

library

Application Midway1 Midway2 Description
SuperLU_dist SuperLU_dist/5.1.0 (default)   SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Distributed version.
SuperLU_mt SuperLU_mt/3.1 (default)   SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Multithreaded (OpenMP) version.
SuperLU_seq SuperLU_seq/5.2.1 (default)   SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Sequential version.
atlas   atlas/3.10.3 (default) Automatically Tuned Linear Algebra Software
CFITSIO cfitsio/3 (default), cfitsio/3+intel-12.1, cfitsio/3+intel-15.0 cfitsio/3, cfitsio/3+gcc-6.2 (default) library for reading and writing data files in FITS data format
GNU Scientific Library (GSL) gsl/1.15, gsl/1.16 (default), gsl/2.2.1+gcc-6.1, gsl/2.2.1+intel-15.0, gsl/2.2.1+intel-16.0 gsl/1.16, gsl/2.2.1 (default), gsl/2.2.1+gcc-6.2, gsl/2.2.1+intel-12.1, gsl/2.2.1+intel-16.0 numerical C/C++ numerical library
lapack   lapack/3.6.1 (default) Linear Algebra PACKage
Metis metis/5.1 (default) metis/5.1 (default) Serial Graph Partitioning and Fill-reducing Matrix Ordering
parmetis parmetis/4.0.3 (default) parmetis/4.0.3+intelmpi-5.1+intel-16.0 (default) Parallel Graph Partitioning and Fill-reducing Matrix Ordering
scalapack   scalapack/2.0.2+openmpi-2.0.1 (default) Scalable Linear Algebra PACKage
tiff   tiff/4.0.6 (default) LibTIFF - TIFF Library and Utilities

machine learning

Application Midway1 Midway2 Description
Nvidia cuDNN cudnn/6.5 (default)   GPU accelerated deep learning
MAchine Learning for LanguagE Toolkit (MALLET) mallet/2.0 (default), mallet/2.0.8RC3   machine learning applications to text
mcl mcl/14.137 (default) mcl/14.137 (default) Markov Cluster Algorithm
OpenCV opencv/2.4 (default), opencv/2.4+python-2.7-2015q1, opencv/3.1 opencv/2.4 (default) computer vision and machine learning software library
Weka weka/3.6 (default)   machine learning algorithms

many-body perturbation theory

Application Midway1 Midway2 Description
BerkeleyGW berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default) berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0, berkeleygw/1.2.0+openmpi-2.0.1 software package for the evaluation of quasiparticle properties and optical responses of materials and molecules

math library

Application Midway1 Midway2 Description
Eigenvalue SoLvers for Petaflop-Applications ELPA elpa/2015.11.001+intelmpi-5.1+intel-16.0 (default) elpa/2015.11.001+intelmpi-5.1+intel-16.0 (default) efficient eigenvalue solver for petaflop applications

mathematics

Application Midway1 Midway2 Description
bertini bertini/1.5.1 (default) bertini/1.5.1 (default) a general-purpose solver, written in C, that was created for research about polynomial continuation
Computational Geometry Algorithms Library (CGAL) cgal/4.1 (default), cgal/4.1+intel-12.1   C++ library for geometric computations
graph-tool graph-tool/2.2 (default)   A Python module for manipulating and analyzing graphs and networks
macaulay2 macaulay2/1.6 (default), macaulay2/1.8 macaulay2/1.6 (default), macaulay2/1.8 software system devoted to supporting research in algebraic geometry and commutative algebra
Mathematica mathematica/10.0, mathematica/10.2, mathematica/8.0, mathematica/9.0 (default) mathematica/10.2 (default) symbolic mathematical software
GNU Octave octave/3.6 (default) octave/4.0 (default) high-level language for numerical computations

media

Application Midway1 Midway2 Description
Blender blender/2.68 (default) blender/2.78a (default) 3D animation suite
FFmpeg ffmpeg/0.11, ffmpeg/1.1 (default), ffmpeg/2.1, ffmpeg/3.0 ffmpeg/3.2 (default) record, convert, and stream audio and video
MPlayer mplayer/stable, mplayer/trunk (default) mplayer/1.3.0 (default) media player
tiff   tiff/4.0.6 (default) LibTIFF - TIFF Library and Utilities
vpx   vpx/1.6 (default)  
x264 x264/stable (default) x264/0.148 (default) application for encoding video streams into H.264/MPEG-4 AVC
x265   x265/2.1 (default) x265

medical

Application Midway1 Midway2 Description
slicer slicer/4.4.0, slicer/4.5.0 (default), slicer/4.6.2 slicer/4.5.0 (default) software platform for the analysis and visualization of medical images and research in image guided therapy

medicine

Application Midway1 Midway2 Description
Basic Local Alignment Search Tool (BLAST) blastplus/2.2 (default) blastplus/2.5 (default) biological search alignment tool
dicom3tools dicom3tools/1 (default) dicom3tools/1 (default) command line utilities for creating, modifying, dumping and validating files of DICOM attributes
MM/PBSA method for GROMACS g_mmpbsa/1.0.0 (default)   calculation of components of binding energy using MM-PBSA method
mpiBLAST mpiblast/trunk (default)   improved implementation of NCBI BLAST, find homology in biological sequences

molecular dynamics

Application Midway1 Midway2 Description
Amber amber/12 (default), amber/14, amber/16, amber/16+cuda-8.0 amber/16 (default) molecular simulations
Adaptive Poisson-Boltzmann Software (APBS) apbs/1.3, apbs/1.4 (default)   analysis of solvation properties of molecules
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
CPMD cpmd/3.15 (default), cpmd/3.17+intelmpi-5.0+intel-15.0 cpmd/3.15+intelmpi-4.0+intel-12.1 (default) parallelized plane wave/pseudopotential implementation of Density Functional Theory
Quantum ESPRESSO espresso/5.1+intel-12.1, espresso/5.1.1+openmpi-1.8+intel-15.0, espresso/5.3.0+intelmpi-5.0+intel-15.0 (default), espresso/5.3.0-west-1.0.2+intelmpi-5.0+intel-15.0, espresso/5.4.0-epw+intelmpi-5.0+intel-15.0, espresso/5.4.0-west-1.1.0+intelmpi-5.0+intel-15.0, espresso/6.0-epw-4.1+intelmpi-5.1+intel-16.0, espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0 espresso/6.0+intelmpi-5.1+intel-16.0 (default), espresso/6.0-west-2.0+intelmpi-5.1+intel-16.0, espresso/6.1+intelmpi-5.1+intel-16.0 suite of codes for electronic-structure calculations and nanoscale materials modeling
MM/PBSA method for GROMACS g_mmpbsa/1.0.0 (default)   calculation of components of binding energy using MM-PBSA method
Gaussian gaussian/09RevA.02 (default), gaussian/09RevB.01, gaussian/09RevD.01 gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01 electronic structure and quantum chemistry
Gromacs gromacs/4.5.5, gromacs/4.6+intel-12.1 (default), gromacs/4.6-cuda+intel-12.1, gromacs/5.0+intelmpi-5.0+intel-15.0, gromacs/5.0-cuda+intelmpi-5.0+intel-15.0   molecular dynamics simulation
Gromacs compiled with PLUMED gromacs-plumed/1.3+intelmpi-4.0+intel-12.1 (default), gromacs-plumed/1.3+openmpi-1.6   gromacs molecular dynamics simulation compiled with plumed free energy calculation
HOOMD-blue hoomd/0.11 (default), hoomd/0.11.0, hoomd/1.0, hoomd/1.1, hoomd/1.1-double, hoomd/1.1-double+intelmpi-5.0+intel-15.0   general-purpose particle simulation toolkit
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) lammps/10Aug2015+intelmpi-5.0+intel-15.0, lammps/9Dec2014+intelmpi-5.0+intel-15.0, lammps/cuda-9Dec2014+intelmpi-5.0+intel-15.0, lammps/trunk (default) lammps/17Nov2016+intelmpi-5.1+intel-16.0 (default) molecular dynamics simulation
NAMD namd/2.10+intelmpi-5.0+intel-15.0, namd/2.10-cuda+intelmpi-5.0+intel-15.0, namd/2.10b1, namd/2.12+intelmpi-5.1+intel-16.0, namd/2.9 (default), namd/2.9-cuda namd/2.11+intelmpi-5.1+intel-16.0 (default), namd/2.12+intelmpi-5.1+intel-16.0 parallel molecular dynamics code for biomolecular system simulation
openbabel openbabel/2.3 (default), openbabel/2.3.1   toolbox for using chemical data
OpenMM openmm/5.2, openmm/6.0 (default), openmm/6.1, openmm/6.2   A toolkit for molecular simulation using high performance GPU code.
PyMol pymol/svn (default) pymol/svn (default) molecular visualization
qbox qbox/1.60+intelmpi-5.0+intel-15.0, qbox/1.63.5+intelmpi-5.1+intel-16.0 (default) qbox/1.63.5+intelmpi-5.1+intel-16.0 (default) scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism

multi media player and framework

Application Midway1 Midway2 Description
vlc vlc/2.0.9 (default)   Application container

multimedia

Application Midway1 Midway2 Description
gstreamer   gstreamer/1.9.90 (default) GStreamer is a library for constructing graphs of media-handling components

natural language processing

Application Midway1 Midway2 Description
EMU Speech Database System emu/cvs (default)   collection of tools for the creation, manipulation and analysis of speech databases
Advanced speech signal processor library (libassp) libassp/1 (default)   handling and analysis for speech signal files
MAchine Learning for LanguagE Toolkit (MALLET) mallet/2.0 (default), mallet/2.0.8RC3   machine learning applications to text
Praat praat/5.3 (default), praat/6.0+gcc-4.8   speech analysis/synthesis/manipulation
Stanford Natural Language Processing (CoreNLP) stanford-nlp/3.3 (default)   natural language processing
word2vec word2vec/trunk (default)   computing vector representations of words

neuroscience

Application Midway1 Midway2 Description
AFNI afni/latest (default) afni/latest (default) neuroimaging data analysis
FreeSurfer freesurfer/5.3 (default) freesurfer/5.3, freesurfer/6.0 (default) analysis and visualization of structural and functional brain imaging data
PyNEST pynest/2.6+python-2.7-2015q1 (default), pynest/2.6-mpi+python-2.7-2015q1   A simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons.
SPM spm/12, spm/8 (default)   statistical parametric mapping

numerical analysis

Application Midway1 Midway2 Description
MINUIT2 Minuit2/5.34 (default), Minuit2/5.34+intel-12.1, Minuit2/5.34+intel-15.0 Minuit2/5.34 (default) library for function minimization
ROOT ROOT/5.26, ROOT/5.34 (default), ROOT/5.34+python-2.7-2014q1, ROOT/6.06 ROOT/5.34.14, ROOT/6.06.08 (default) program library for particle physics data analysis
SuiteSparse SuiteSparse/4.0 (default), SuiteSparse/4.0+intel-12.1, SuiteSparse/4.2   sparse matrix algorithms
Armadillo armadillo/5.0, armadillo/5.0+intel-15.0, armadillo/7.5 (default), armadillo/7.6, armadillo/7.8 armadillo/7.5 (default), armadillo/7.6, armadillo/7.8 C++ linear algebra software library
Class Library for High Energy Physics (CLHEP) clhep/2.2 (default) clhep/2.3 (default) C++ mathematical library for high energy physics analysis
CSDP csdp/dev+intel-12.1 (default)   a C library for semidefinite programming
eigen eigen/3.2 (default) eigen/3.2 (default) C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
Fastest Fourier Transform in the West (FFTW v2) fftw2/2.1.5 (default), fftw2/2.1.5+intel-12.1, fftw2/2.1.5+intelmpi-4.0, fftw2/2.1.5+intelmpi-4.0+intel-12.1, fftw2/2.1.5+mvapich2-1.9, fftw2/2.1.5+openmpi-1.6, fftw2/2.1.5+openmpi-1.6+intel-12.1, fftw2/2.1.5+openmpi-1.6+pgi-2012, fftw2/2.1.5+pgi-2012   computation of discrete Fourier transform
Fastest Fourier Transform in the West (FFTW v3) fftw3/3.3 (default), fftw3/3.3+intel-12.1, fftw3/3.3+intel-13.1, fftw3/3.3+intel-15.0, fftw3/3.3+intelmpi-4.0, fftw3/3.3+intelmpi-4.0+intel-12.1, fftw3/3.3+intelmpi-4.1+intel-13.1, fftw3/3.3+intelmpi-5.0+intel-15.0, fftw3/3.3+mvapich2-1.9, fftw3/3.3+mvapich2-1.9+intel-12.1, fftw3/3.3+mvapich2-1.9+pgi-2012, fftw3/3.3+openmpi-1.6, fftw3/3.3+openmpi-1.6+intel-12.1, fftw3/3.3+openmpi-1.6+pgi-2012, fftw3/3.3+pgi-2012, fftw3/3.3.5+intelmpi-5.0+intel-15.0, fftw3/3.3.5+intelmpi-5.1+intel-16.0, fftw3/3.3.6+intelmpi-5.1+intel-16.0 fftw3/3.3.5 (default), fftw3/3.3.5+intelmpi-4.0+intel-12.1, fftw3/3.3.5+intelmpi-5.1+intel-16.0, fftw3/3.3.5+openmpi-2.0.1 computation of discrete Fourier transform
graph-tool graph-tool/2.2 (default)   A Python module for manipulating and analyzing graphs and networks
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
GNU Scientific Library (GSL) gsl/1.15, gsl/1.16 (default), gsl/2.2.1+gcc-6.1, gsl/2.2.1+intel-15.0, gsl/2.2.1+intel-16.0 gsl/1.16, gsl/2.2.1 (default), gsl/2.2.1+gcc-6.2, gsl/2.2.1+intel-12.1, gsl/2.2.1+intel-16.0 numerical C/C++ numerical library
Interior Point OPTimizer (Ipopt) ipopt/3.11 (default)   large-scale non-linear optimization
KNITRO knitro/10.0, knitro/10.1, knitro/10.2, knitro/9.0.1-z (default), knitro/9.1.0-z knitro/10.1.0 (default), knitro/10.2 for large-scale optimization
Intel Math Kernel Library (MKL) mkl/10.2, mkl/10.3 (default), mkl/11.0, mkl/11.1, mkl/11.2, mkl/11.3, mkl/2017 mkl/10.3, mkl/11.2, mkl/11.3, mkl/2017 (default) library of optimized numerical routines
GNU MPFR Library (MPFR) mpfr/3.1 (default) mpfr/3.1.4 (default), mpfr/3.1.4+gcc-6.2 A C library for multiple-precision floating-point computations
MUltifrontal Massively Parallel sparse direct Solver (MUMPS) mumps/4.10 (default)   parallel sparse direct solver
GNU Octave octave/3.6 (default) octave/4.0 (default) high-level language for numerical computations
OpenBLAS openblas/0.2.6 (default)   optimized BLAS library
PETSc petsc/3.4+openmpi-1.6 (default), petsc/3.6+intelmpi-5.0+intel-15.0 petsc/3.7.4+openmpi-2.0.1 (default) data analysis for scientific applications of partial differential equation models
pyFFTW pyfftw/0.9.2+python-2.7-2014q3 (default)   A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.
SemiDefinite Programming Algorithm (SDPA) sdpa/7.3.8+intel-12.1 (default)   optimization algorithm
SemiDefinite Programming Algorithm Double-Double (SDPA-DD) sdpa-dd/7.1.2+intel-12.1 (default)   semidefinite programming with pseudo double-double precision arithmetic
SemiDefinite Programming Algorithm (SDPA-GMP) sdpa-gmp/7.1.2+intel-12.1 (default)   semidefinite programming with arbitrary precision arithmetic
SemiDefinite Programming Algorithm Quad-Double (SDPA-QD) sdpa-qd/7.1.2+intel-12.1 (default)   semidefinite programming with pseudo quad-double precision arithmetic

optimization

Application Midway1 Midway2 Description
PyGMO PyGMO/current+intelmpi-5.1+intel-16.0 (default) PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) Python Parallel Global Multiobjective Optimizer

parallel

Application Midway1 Midway2 Description
PyGMO PyGMO/current+intelmpi-5.1+intel-16.0 (default) PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) Python Parallel Global Multiobjective Optimizer

parser

Application Midway1 Midway2 Description
ANother Tool for Language Recognition (ANTLR) antlr/2.7 (default) antlr/2.7.7 (default) parser generator for computer-based language recognition

performance analysis

Application Midway1 Midway2 Description
HPCToolkit hpctoolkit/5.3 (default), hpctoolkit/5.3+intel-12.1, hpctoolkit/5.3+intelmpi-4.0, hpctoolkit/5.3+openmpi-1.6   measurement and analysis of program performance on high-performance computers
hpcviewer hpcviewer/5.3 (default) hpcviewer/5.3, hpcviewer/5.4 (default) graphical user interface that interactively presents performance data from hpctoolkit
PAPI papi/5.1, papi/5.3 (default) papi/5.5 (default) standard API for accessing hardware performance counters
Valgrind valgrind/3.7, valgrind/3.8, valgrind/3.9 (default) valgrind/3.12+gcc-6.2 (default) debugging and profiling tools, most commonly used to locate memory errors, including leaks, but also can be used to debug threaded codes and profile cache efficiency.

physics

Application Midway1 Midway2 Description
gpaw gpaw/0.10+intelmpi-5.0+intel-15.0 (default)   Density-functional theory python code
harminv harminv/1.4 (default) harminv/1.4 (default) A free program (and accompanying library) to solve the problem of harmonic inversion.
meep meep/1.3 (default), meep/1.3+intelmpi-5.0+intel-15.0   A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
multinest multinest/3.10 (default)   MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.
openmx openmx/3.7 (default)   A software package for nano-scale material simulations based on density functional theories, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.
xc xc/2.2+intel-15.0 (default)   C library for density-functional theory
xcrysden xcrysden/1.5 (default) xcrysden/1.5 (default) XCrySDen is a crystalline and molecular structure visualization program

population

Application Midway1 Midway2 Description
Migrate-n migrate-n/3.6 (default)   estimation of population size and gene flow

proteins

Application Midway1 Midway2 Description
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
MM/PBSA method for GROMACS g_mmpbsa/1.0.0 (default)   calculation of components of binding energy using MM-PBSA method
Gromacs gromacs/4.5.5, gromacs/4.6+intel-12.1 (default), gromacs/4.6-cuda+intel-12.1, gromacs/5.0+intelmpi-5.0+intel-15.0, gromacs/5.0-cuda+intelmpi-5.0+intel-15.0   molecular dynamics simulation
HOOMD-blue hoomd/0.11 (default), hoomd/0.11.0, hoomd/1.0, hoomd/1.1, hoomd/1.1-double, hoomd/1.1-double+intelmpi-5.0+intel-15.0   general-purpose particle simulation toolkit
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) lammps/10Aug2015+intelmpi-5.0+intel-15.0, lammps/9Dec2014+intelmpi-5.0+intel-15.0, lammps/cuda-9Dec2014+intelmpi-5.0+intel-15.0, lammps/trunk (default) lammps/17Nov2016+intelmpi-5.1+intel-16.0 (default) molecular dynamics simulation
mpiBLAST mpiblast/trunk (default)   improved implementation of NCBI BLAST, find homology in biological sequences
NAMD namd/2.10+intelmpi-5.0+intel-15.0, namd/2.10-cuda+intelmpi-5.0+intel-15.0, namd/2.10b1, namd/2.12+intelmpi-5.1+intel-16.0, namd/2.9 (default), namd/2.9-cuda namd/2.11+intelmpi-5.1+intel-16.0 (default), namd/2.12+intelmpi-5.1+intel-16.0 parallel molecular dynamics code for biomolecular system simulation
openbabel openbabel/2.3 (default), openbabel/2.3.1   toolbox for using chemical data
RAPSearch rapsearch/2 (default)   Reduced Alphabet based Protein similarity Search

python

Application Midway1 Midway2 Description
PyGMO PyGMO/current+intelmpi-5.1+intel-16.0 (default) PyGMO/current, PyGMO/current+gcc-6.2, PyGMO/current+intelmpi-5.1+intel-16.0 (default) Python Parallel Global Multiobjective Optimizer

simulation

Application Midway1 Midway2 Description
abaqus abaqus/6.14 (default)   engineering simulations
abinit abinit/7.10 (default)   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.
Amber amber/12 (default), amber/14, amber/16, amber/16+cuda-8.0 amber/16 (default) molecular simulations
comsol comsol/52a, comsol/53 (default) comsol/52a, comsol/53 (default) physics simulations
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
gate gate/7.1 (default)   Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy
Geant4 geant4/10.00 (default), geant4/10.01, geant4/10.02+gcc-4.8 geant4/10.01 (default) a toolkit for the simulation of particles through matter
Gromacs gromacs/4.5.5, gromacs/4.6+intel-12.1 (default), gromacs/4.6-cuda+intel-12.1, gromacs/5.0+intelmpi-5.0+intel-15.0, gromacs/5.0-cuda+intelmpi-5.0+intel-15.0   molecular dynamics simulation
HOOMD-blue hoomd/0.11 (default), hoomd/0.11.0, hoomd/1.0, hoomd/1.1, hoomd/1.1-double, hoomd/1.1-double+intelmpi-5.0+intel-15.0   general-purpose particle simulation toolkit
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) lammps/10Aug2015+intelmpi-5.0+intel-15.0, lammps/9Dec2014+intelmpi-5.0+intel-15.0, lammps/cuda-9Dec2014+intelmpi-5.0+intel-15.0, lammps/trunk (default) lammps/17Nov2016+intelmpi-5.1+intel-16.0 (default) molecular dynamics simulation
libctl libctl/3.2.2 (default)   A Guile-based library implementing flexible control files for scientific simulations.
meep meep/1.3 (default), meep/1.3+intelmpi-5.0+intel-15.0   A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
NAMD namd/2.10+intelmpi-5.0+intel-15.0, namd/2.10-cuda+intelmpi-5.0+intel-15.0, namd/2.10b1, namd/2.12+intelmpi-5.1+intel-16.0, namd/2.9 (default), namd/2.9-cuda namd/2.11+intelmpi-5.1+intel-16.0 (default), namd/2.12+intelmpi-5.1+intel-16.0 parallel molecular dynamics code for biomolecular system simulation
OpenMM openmm/5.2, openmm/6.0 (default), openmm/6.1, openmm/6.2   A toolkit for molecular simulation using high performance GPU code.
openmx openmx/3.7 (default)   A software package for nano-scale material simulations based on density functional theories, norm-conserving pseudopotentials, and pseudo-atomic localized basis functions.
Parallel Ice Sheet Model (PISM) pism/0.6 (default)   ice sheet model
PyNEST pynest/2.6+python-2.7-2015q1 (default), pynest/2.6-mpi+python-2.7-2015q1   A simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons.
siesta siesta/3.2 (default), siesta/trunk-462   SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids
wannier90 wannier90/2.0 (default)   Maximally localized Wannier functions.

statistics

Application Midway1 Midway2 Description
R R/2.15, R/2.15+intel-12.1, R/3.0, R/3.0+intel-12.1, R/3.1, R/3.1+intel-15.0, R/3.2 (default), R/3.2+intel-15.0, R/3.3.2 R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4 (default) programming language/environment for statistical computation and graphics
BEAGLE beagle/trunk (default) beagle/trunk (default) library for core calculations with phylogenetics packages
graph-tool graph-tool/2.2 (default)   A Python module for manipulating and analyzing graphs and networks
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
jags jags/4.0.1 (default), jags/4.2.0 jags/4.2.0 (default) JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
MAchine Learning for LanguagE Toolkit (MALLET) mallet/2.0 (default), mallet/2.0.8RC3   machine learning applications to text
multinest multinest/3.10 (default)   MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions.
PRISM prism/4.0 (default)   probabilistic model checker
Randomized Axelerated Maximum Likelihood (RAxML) raxml/trunk (default)   sequential and parallel Maximum Likelihood based inference of large phylogenetic trees
sas sas/9.4 (default)   business intelligence software
Stata stata/13 (default), stata/14 stata/14 (default) data analysis and statistical software

system

Application Midway1 Midway2 Description
Mobile shell (Mosh) mosh/1.2 (default) mosh/1.2.6 (default) connect to server from client to run remote terminal (like SSH)
proot proot/current (default) proot/current (default) user-space implementation of chroot, mount –bind, and binfmt_misc
Tree tree/1.6.0 (default)   recursive directory listing command
YAZ yaz/5.4 (default) yaz/5.20 (default) Z39.50/SRW/SRU client and server development toolkit

testing

Application Midway1 Midway2 Description
check   check/0.10.0 (default) Check is a unit testing framework for C

text

Application Midway1 Midway2 Description
pandoc pandoc/1.13+ghc-7.8 (default) pandoc/1.13 (default) Document converter supporting many markup formats
poppler poppler/0.31.0 (default)   pdf library and utilities
tkdiff tkdiff/4.2 (default)   graphical interface for diff
xpdf xpdf/3.04 (default) xpdf/3.04 (default) pdf viewer and utilities

text editor

Application Midway1 Midway2 Description
GNU Emacs emacs/23.4, emacs/24 (default) emacs/25 (default) GNU Emacs text editor
GNOME text editor (gedit) gedit/2.28 (default)   text editor
vim vim/7.3, vim/7.4 (default) vim/7.4 (default) advanced text editor

typesetting

Application Midway1 Midway2 Description
TeX Live texlive/2012, texlive/2016 (default) texlive/2016, texlive/2017 (default) TeX typesetting system, including extensions (etex, latex, pdflatex, etc.)

version control

Application Midway1 Midway2 Description
git git/2.7 (default) git/2.10 (default) distributed version control system
git-lfs git-lfs/1.3 (default) git-lfs/1.4 (default) an open source git extension for versioning large files
Mercurial mercurial/2.5 (default), mercurial/2.8, mercurial/3.1 mercurial/4.0 (default) distributed version control system
Subversion subversion/1.6, subversion/1.7, subversion/1.8 (default), subversion/keyring subversion/1.9.4 (default) version control system

video

Application Midway1 Midway2 Description
Blender blender/2.68 (default) blender/2.78a (default) 3D animation suite
FFmpeg ffmpeg/0.11, ffmpeg/1.1 (default), ffmpeg/2.1, ffmpeg/3.0 ffmpeg/3.2 (default) record, convert, and stream audio and video
MPlayer mplayer/stable, mplayer/trunk (default) mplayer/1.3.0 (default) media player
vpx   vpx/1.6 (default)  
x264 x264/stable (default) x264/0.148 (default) application for encoding video streams into H.264/MPEG-4 AVC
x265   x265/2.1 (default) x265

video/audio

Application Midway1 Midway2 Description
Bino bino/1.4 (default) bino/1.4 (default) 3D video player
FFmpeg ffmpeg/0.11, ffmpeg/1.1 (default), ffmpeg/2.1, ffmpeg/3.0 ffmpeg/3.2 (default) record, convert, and stream audio and video
libav libav/11.4 (default)   A package of libraries for dealing with a variety of multimedia formats.
mpg123 mpg123/1.13, mpg123/1.14 (default) mpg123/1.13 (default), mpg123/1.14 MPEG audio player and decoder
MPlayer mplayer/stable, mplayer/trunk (default) mplayer/1.3.0 (default) media player
x264 x264/stable (default) x264/0.148 (default) application for encoding video streams into H.264/MPEG-4 AVC

visualization

Application Midway1 Midway2 Description
ANTs ANTs/2.1 (default)   Advanced Normalization Tools for biomedical image analysis
ROOT ROOT/5.26, ROOT/5.34 (default), ROOT/5.34+python-2.7-2014q1, ROOT/6.06 ROOT/5.34.14, ROOT/6.06.08 (default) program library for particle physics data analysis
MapRes ResMap/1.1.4 (default) ResMap/1.1.4 (default) ResMap (Resolution Map) is a Python (NumPy/SciPy) application with a Tkinter GUI and a command-line interface. It is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryoEM).
Blender blender/2.68 (default) blender/2.78a (default) 3D animation suite
CP2K cp2k/2.4 (default), cp2k/4.1+intelmpi-5.1+intel-16.0, cp2k/svn cp2k/4.1+intelmpi-5.1+intel-16.0 (default) simulations of solid state, liquid, molecular, and biological systems
Cytoscape Web cytoscape/2.8 (default)   network visualization library
Diderot diderot/trunk, diderot/vis12 (default)   parallel domain-specific language for image analysis and visualization
ferret ferret/6.9 (default) ferret/6.9 (default) An interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data set
FreeSurfer freesurfer/5.3 (default) freesurfer/5.3, freesurfer/6.0 (default) analysis and visualization of structural and functional brain imaging data
Gephi gephi/0.8 (default) gephi/0.9 (default) visualization and exploration of network data
gnuplot gnuplot/4.4, gnuplot/4.6 (default) gnuplot/5.0 (default) portable command-line driven graphing utility
Grace grace/5.1 (default) grace/5.1 (default) plotting 2D data
GrADS grads/1.8, grads/1.9, grads/2.0 (default) grads/2.0 (default) manipulation and visualization of earth science data
graph-tool graph-tool/2.2 (default)   A Python module for manipulating and analyzing graphs and networks
Graph Visualization Software (Graphviz) graphviz/2.28 (default) graphviz/2.28, graphviz/2.38 (default) graph visualization software
grass grass/6.4 (default) grass/6.4 (default) geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization
Hierarchical Equal Area isoLatitude Pixelization of a sphere (HEALPix) healpix/2.20, healpix/3.11 (default), healpix/3.20, healpix/3.20+intel-15.0 healpix/3.31 (default) pixelization of subdivision of spherical surface in which each pixel covers the same surface area as every other pixel
IDL idl/8.2 (default) idl/8.2 (default) scientific programming language for visualization
Ionization FRont Interactive Tool (IFrIT) ifrit/3.4 (default)   3D visualization software focused on cosmological simulations
itk itk/4.10 (default), itk/4.11, itk/4.11+python-2.7-2015q2   cross-platform, open-source application development framework widely used for the development of image segmentation and image registration
Java 3D (j3d) j3d/1.5 (default)   3D API for Java
NCAR Command Language (NCL) ncl_ncarg/6.1 (default), ncl_ncarg/6.2, ncl_ncarg/6.3 ncl_ncarg/6.2 (default) interpreted language designed for data analysis and visualization
Ncview ncview/2.1.1 (default)   visual browser netCDF format files
GNU Octave octave/3.6 (default) octave/4.0 (default) high-level language for numerical computations
OpenCV opencv/2.4 (default), opencv/2.4+python-2.7-2015q1, opencv/3.1 opencv/2.4 (default) computer vision and machine learning software library
panoply panoply/4 (default)   Panoply is a cross-platform application that plots geo-gridded and other arrays from netCDF, HDF, GRIB, and other datasets.
ParaView   paraview/4.4 (default) Multi-platform data analysis and visualization application
pgplot pgplot/5.2 (default) pgplot/5.2 (default) Fortran- or C-callable, device-independent graphics package for making simple scientific graphs
Parallel Ice Sheet Model (PISM) pism/0.6 (default)   ice sheet model
PyMol pymol/svn (default) pymol/svn (default) molecular visualization
Teem teem/trunk (default) teem/trunk (default) scientific raster data visualization
VisIt visit/2.6 (default), visit/all   data visualization, animation, and analysis
vmd vmd/1.9, vmd/1.9.1, vmd/1.9.2 (default) vmd/1.9.2 (default) molecular visualization program
Visualization Toolkit (VTK) vtk/5.10, vtk/5.10+python-2.7-2014q1, vtk/5.8 (default), vtk/7.1, vtk/7.1+python-2.7-2015q2 vtk/7.0 (default), vtk/7.1+python-2.7.12 3D computer graphics, image processing, and visualization
xcrysden xcrysden/1.5 (default) xcrysden/1.5 (default) XCrySDen is a crystalline and molecular structure visualization program
yt yt/3.0 (default), yt/3.1 yt/3.3 (default) visualization and analysis tool for cosmological data

workflow

Application Midway1 Midway2 Description
CCTools cctools/3.6 (default)   collection of software for harnessing large scale distributed systems
Connect Client connect-client/0.5.2 (default)   Set of programs and files for linking a campus research computing cluster to a CI Connect instance which uses HTCondor to submit jobs to the Open Science Grid
GNU Parallel parallel/latest (default) parallel/latest (default) shell tool for executing jobs in parallel
Swift swift/0.94.1, swift/0.95 (default), swift/0.96, swift/testing swift/0.95 (default) workflow scripting language