Software Modules

All software available via the modules system on Midway2 are listed on this page. To load any particular software module shown below use the following syntax from the command line on Midway2:

[jbravo@midway2 ~]$ module load <modulename>

where <modulename> is the name of the software module.

See the page Using software modules on Midway for more information.

GUI

Application Version Description
fltk fltk/1.3.4 (default) FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X
xdiskusage xdiskusage/1.51 (default) Graphical display of disk usage

R

Application Version Description
R R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default) The R language and environment for statistical computing and graphics.

alignment

Application Version Description
muscle muscle/3.8.31 (default) MUSCLE is one of the best-performing multiple alignment programs

array

Application Version Description
swarm swarm/latest (default) Swarm reads a list of command lines then submits all command scripts to the cluster as a Slurm job array

assembler

Application Version Description
glew glew/1.9, glew/2.0.0 (default) The OpenGL Extension Wrangler Library
nasm nasm/2.13.01+gcc-6.2 (default) The Netwide Assembler
yasm yasm/1.3.0 (default) The Yasm Modular Assembler Project

astrophysics

Application Version Description
Fermi Science Tools fermi-fssc/v10r0p5 (default) suite of tools for the analysis of both LAT and GBM data
snid snid/5.0 (default) Supernova Identification software

bioinformatics

Application Version Description
MACS MACS/1.4 (default) Model-based Analysis for ChIP-Seq
MEME MEME/4.11 (default) Motif-based sequence analysis tools.
RSEM RSEM/1.3 (default) Accurate quantification of gene and isoform expression from RNA-Seq data.
blast blast/2.9.0 (default) BLAST+: command-line tools for Basic Local Alignment Search
bowtie bowtie/1.1.2, bowtie/1.2.1.1 (default) DNA sequence alignment software
bs-cli bs-cli/0.9.17 (default) BaseSpace Sequence Hub CLI
bwa bwa/0.7.15 (default) Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
clark clark/1.2.3.1 (default) Fast, accurate and versatile sequence classification system
gatk gatk/3.7 (default) Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data
gcta gcta/1.91.2, gcta/1.92.2 (default) Software for genome-wide complex trait analysis.
Integrative Genomics Viewer Tools igv/2.4.11 (default) A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Integrative Genomics Viewer Tools igvtools/2.3.98 (default) Accompanying CLI tools for IGV
picard picard/2.18.15 (default), picard/2.18.2 A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
tophat tophat/2.1 (default) splice junction mapper for RNA-Seq reads

biology

Application Version Description
bcftools bcftools/1.4.1 (default) BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools.
bcl2fastq2 bcl2fastq2/2.20 (default) Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.
BEAGLE beagle/trunk (default) library for core calculations with phylogenetics packages
BEAST beast/1.8 (default) Bayesian analysis of molecular sequences
blast blast/2.9.0 (default) BLAST+: command-line tools for Basic Local Alignment Search
bowtie bowtie/1.1.2, bowtie/1.2.1.1 (default) DNA sequence alignment software
bowtie2 bowtie2/2.2.9 (default) DNA sequence alignment software
breseq breseq/0.32.0 (default) Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes.
cellranger cellranger/2.1.1 (default), cellranger/3.0.0 An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats.
cufflinks cufflinks/2.2 (default) Transcriptome assembly and differential expression analysis for RNA-Seq.
ea-utils ea-utils/current (default) Command-line tools for processing biological sequencing data
fastqc fastqc/0.11.5 (default) A quality control tool for high throughput sequence data.
fasttree 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) A collection of command-line tools for FASTA sequence files preprocessing
fsl fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default) FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
hmmer hmmer/3.1b2 (default) HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
htslib htslib/1.4.1 (default) C library for high-throughput sequencing data formats; originally distributed with samtools.
Integrative Genomics Viewer Tools igv/2.4.11 (default) A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Integrative Genomics Viewer Tools igvtools/2.3.98 (default) Accompanying CLI tools for IGV
mafft mafft/7.310 (default) Multiple alignment program for amino acid or nucleotide sequences
mothur 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) This program corrects whole frame image motion recordded with dose fractionated image stack.
muscle muscle/3.8.31 (default) MUSCLE is one of the best-performing multiple alignment programs
openbabel openbabel/2.3 (default), openbabel/2.4 toolbox for using chemical data
openbabel openbabel_nopy/2.3 (default) toolbox for using chemical data
Rosetta rosetta/2017.08.59291 (default) The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
samtools samtools/1.2, samtools/1.4.1, samtools/1.9 (default) Tools written in C using htslib for manipulating next-generation sequencing data.
tophat tophat/2.1 (default) splice junction mapper for RNA-Seq reads
treePL treepl/git (default) phylogenetic penalized likelihood program
vmd vmd/1.9.2 (default) molecular visualization program

browser

Application Version Description
firefox firefox/67.0 (default), firefox/esr web browser

checkpointing

Application Version Description
dmtcp dmtcp/2.5 (default) Distributed MultiThreaded CheckPointing

chemistry

Application Version Description
Atomic Simulation Environment (ASE) ase/3.16 (default) ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
avogadro avogadro/1.2.0 (default) Molecule editor and visualization tool
BerkeleyGW berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0 software package for the evaluation of quasiparticle properties and optical responses of materials and molecules
crux crux/3.2 (default) Analysis tools for interpreting protein mass spectrometry data
DeePMD deepmd/0.12.4 (default) Package for building deep learning based models of interatomic potential energy and force field
mkl/2017 dftbplus/18.1+intelmpi-2017.up4+intel-17.0 (default) Density Functional based Tight Binding (DFTB) method
Quantum ESPRESSO 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, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 Suite of codes for electronic-structure calculations and nanoscale materials modeling
Gaussian gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01, gaussian/16RevA.03 electronic structure and quantum chemistry
i-pi i-pi/2.0 (default) A Universal Force Engine for Advanced Molecular Dynamics
Jmol jmol/14.29 (default) molecular viewer and editor
NWChem nwchem/6.6+intelmpi-5.1+intel-16.0 (default) Software toolkit for computational chemistry
openbabel openbabel/2.3 (default), openbabel/2.4 toolbox for using chemical data
openbabel openbabel_nopy/2.3 (default) toolbox for using chemical data
Orca orca/3.0 (default), orca/4.0, orca/4.1 Quantum Chemistry Electronic Structure Package
Pathways Program in Molecular Engineering Env settings ppme/1.0 (default) Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering
pyscf pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 Python Module for Quantum Chemistry
wannier90 wannier90/3.0 (default) Maximally localized Wannier functions.

climate

Application Version Description
Climate Data Operators (CDO) cdo/1.6, cdo/1.9 (default) Analysis of climate and NWP model data.

cloud computing

Application Version Description
cloud cloud/1.0 (default) RCC Cloud Connector

compilers

Application Version Description
ant ant/1.8.4 (default), ant/1.9.7 Java library and command-line tool for building Java applications
berkeley_upc berkeley_upc/2.26 (default) An extension of the C programming language designed for high performance computing on large-scale parallel machines
clang clang/3.8.0, clang/3.9 (default), clang/7.1.0+gcc-6.1 C compiler from LLVM project
GNU Compiler Collection (GCC) gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0 C/C++/Fortran compiler suite
Intel Parallel Studio intel/12.1, intel/15.0, intel/16.0 (default), intel/17.0, intel/18.0, intel/18.0.5, intel/19.0.1 C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
java java/1.7, java/1.8 (default), java/11.0.1 programming language
julia julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0 (default) The Julia dynamic programming language for technical computing.
m4 m4/1.4.18 (default) Implementation of the traditional Unix macro processor.
PGI Compiler Suite pgi/2016, pgi/2017 (default) C/C++/Fortran compiler suite
racket racket/6.7 (default) full-spectrum programming language

compression

Application Version Description
lzo lzo/2.10 (default) LZO is a portable lossless data compression library written in ANSI C.

computation

Application Version Description
octave octave/4.0 (default) High-level interpreted language for numerical computations

computer architecture

Application Version Description
gem5 gem5/2015-09-03 (default) Modular platform for computer-system architecture research, encompassing system-level architecture as well as processor microarchitecture.

container

Application Version Description
singularity singularity/2.5.2 (default), singularity/3.0.1 Container

copy

Application Version Description
xclip xclip/latest+gcc-6.2 (default) xclip provides an interface to X selections from the command line
xsel xsel/latest+gcc-6.2 (default) XSel is a command-line program for getting and setting the contents of the X selection

data

Application Version Description
redis cassandra/3.11.3 (default) A key-value cache and store server
cfitsio cfitsio/3, cfitsio/3+gcc-6.2 (default), cfitsio/3.450 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
curl curl/7.50 (default) tool and library for transferring data over the internet
ferret 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
cfitsio flask/git (default) CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
HDF5 hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.8, 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-2.0.1, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0, hdf5/1.8.20+intelmpi-5.1+intel-16.0 data model, library, and file format for storing and managing data
HDF5 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
lzo lzo/2.10 (default) LZO is a portable lossless data compression library written in ANSI C.
mysql-workbench mysql_workbench/6.3 (default) mysql GUI client
netcdf netcdf/3.6.3+intel-12.1, netcdf/4.2+intel-12.1, 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, netcdf/4.4.1.1-c-fortran+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/4.4.4 (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.
nosqlbooster4mongo nosqlbooster4mongo/4.7.4 (default) nosqlbooster4mongo
openbabel openbabel/2.3 (default), openbabel/2.4 toolbox for using chemical data
openbabel openbabel_nopy/2.3 (default) toolbox for using chemical data
openrefine openrefine/3.0 (default) openrefine
pnetcdf pnetcdf/1.11.0 (default) High-performance parallel I/O library for accessing files in format compatibility with Unidata’s NetCDF.
redis redis/3.2, redis/4.0.11 (default) A key-value cache and store server
spark spark/2.0.2, spark/2.1 (default), spark/2.2, spark/2.2.1, spark/2.2_mkl, spark/2.3.0, spark/2.3.2, spark/2.4.3 Apache Spark is a fast and general engine for large-scale data processing.
sra_toolkit sra_toolkit/2.6, sra_toolkit/2.8 (default) a collection of tools and libraries for using data in the INSDC Sequence Read Archives
tensorflow tensorflow_c_gpu/1.8 (default) tensorflow, C API, GPU
treePL treepl/git (default) phylogenetic penalized likelihood program
UnRAR unrar/5.4 (default) utility for extracting rar format archives
Xerces-C++ XML Parser xerces/2.8.0, xerces/3.1.4 (default) validating XML parser written in C++

data analysis

Application Version Description
ROOT ROOT/5.34.14, ROOT/6.06.08 (default), ROOT/6.10.02+gcc-6.2, ROOT/6.16.00 An object oriented framework for large scale data analysis
CLUTO cluto/2.1 (default) clustering low- and high-dimensional datasets and for analysis of various clusters
hmmer hmmer/3.1b2 (default) HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
jags jags/4.2.0 (default) JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
sra_toolkit 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) scientific raster data visualization

database

Application Version Description
leveldb caffe/git (default) LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values
redis cassandra/3.11.3 (default) A key-value cache and store server
HDF5 hdf5/1.10.0-patch1+intelmpi-5.1+intel-16.0, hdf5/1.8, 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-2.0.1, hdf5/1.8.16+openmpi-2.0.2+gcc-6.2, hdf5/1.8.17 (default), hdf5/1.8.17+intel-16.0, hdf5/1.8.20+intelmpi-5.1+intel-16.0 data model, library, and file format for storing and managing data
HDF5 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 is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments.
leveldb leveldb/git (default) LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values
lmdb lmdb/git (default) Lightning Memory-Mapped Database from Symas
mysql mysql/5.6 (default) MySQL database server
mysql-workbench mysql_workbench/6.3 (default) mysql GUI client
nosqlbooster4mongo nosqlbooster4mongo/4.7.4 (default) nosqlbooster4mongo
openrefine openrefine/3.0 (default) openrefine
pnetcdf pnetcdf/1.11.0 (default) High-performance parallel I/O library for accessing files in format compatibility with Unidata’s NetCDF.
redis redis/3.2, redis/4.0.11 (default) A key-value cache and store server

debugging

Application Version Description
Allinea Performance Reports PerformanceReports/7.0 (default) profiler
DDD ddd/3.3+gcc-6.2 (default) GNU DDD is a graphical front-end for command-line debuggers
Allinea DDT ddt/5.0, ddt/7.0 (default) debugger
ARM (former Allinea) forge (ddt, map) forge/18.0.1 (default) debugger and profiler
GNU Debugger (GDB) 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/3.12+gcc-6.2 (default) Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.

deep-learning

Application Version Description
DeePMD deepmd/0.12.4 (default) Package for building deep learning based models of interatomic potential energy and force field
JAX jax/0.1.39 (default) Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

development

Application Version Description
Anaconda2 Anaconda2/2019.03, Anaconda2/4.3.0 (default), Anaconda2/5.1.0 Anaconda2 python distribution
Anaconda3 Anaconda3/2018.12, Anaconda3/2019.03, Anaconda3/4.1.1, Anaconda3/4.3.0 (default), Anaconda3/5.0.0.1, Anaconda3/5.0.1, Anaconda3/5.1.0, Anaconda3/5.3.0 Anaconda3 python distribution
IntelPython2 IntelPython2/2018.1.023 (default) Intel distribution of python
IntelPython3 IntelPython3/2018.1.023 (default) Intel distribution of python
Allinea Performance Reports PerformanceReports/7.0 (default) profiler
R R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default) The R language and environment for statistical computing and graphics.
UCLAPhonotacticLearner UCLAPhonotacticLearner/latest (default) A Maximum Entropy Model of Phonotactics and Phonotactic Learning
ant ant/1.8.4 (default), ant/1.9.7 Java library and command-line tool for building Java applications
Autoconf autoconf/2.68 (default) configures software source code packages
Bash Automated Testing System (BATS) bats/latest (default) TAP compliant testing framework for bash
bazel bazel/0.13.0, bazel/0.5.0, bazel/0.5.1 (default) Bazel is Google’s own build tool
berkeley_upc berkeley_upc/2.26 (default) An extension of the C programming language designed for high performance computing on large-scale parallel machines
binutils binutils/2.28+gcc-6.2 (default) binutils
Boost boost/1.50, boost/1.51.0, boost/1.61, 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, boost/1.64.0, boost/1.66.0 (default), boost/1.68.0 Portable C++ source libraries.
check check/0.10.0 (default) Check is a unit testing framework for C
clang clang/3.8.0, clang/3.9 (default), clang/7.1.0+gcc-6.1 C compiler from LLVM project
cmake cmake/3.11.0 (default), cmake/3.6.2 Cross-platform build system.
Nvidia CUDA Toolkit cuda/10.0, cuda/6.5 (default), cuda/7.5, cuda/8.0, cuda/9.0, cuda/9.0a, cuda/9.1 parallel computing platform and programming model
DDD ddd/3.3+gcc-6.2 (default) GNU DDD is a graphical front-end for command-line debuggers
Allinea DDT ddt/5.0, ddt/7.0 (default) debugger
dos2unix dos2unix/7.3.5 (default) Dos2Unix / Unix2Dos - Text file format converters
ARM (former Allinea) forge (ddt, map) forge/18.0.1 (default) debugger and profiler
GNU Compiler Collection (GCC) gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0 C/C++/Fortran compiler suite
gcj gcj/6.2+gcc-6.2 (default) GNU implementation of java
GNU Debugger (GDB) 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.
git-lfs git-lfs/1.4 (default) an open source git extension for versioning large files
glew glew/1.9, glew/2.0.0 (default) The OpenGL Extension Wrangler Library
gsl 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, gsl/2.5 The GNU scientific library
haskell-stack haskell-stack/1.1 (default) cross-platform program for developing Haskell projects
Intel Parallel Studio intel/12.1, intel/15.0, intel/16.0 (default), intel/17.0, intel/18.0, intel/18.0.5, intel/19.0.1 C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
java java/1.7, java/1.8 (default), java/11.0.1 programming language
julia julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0 (default) The Julia dynamic programming language for technical computing.
libedit libedit/0.3 (default) Non-GPL replacement for readline library. A spin-off from NetBSD code. Aim is for 100% readline API compatibility
libevent libevent/2.1.8 (default) The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts
libfabric libfabric/1.7.0 (default) Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications
libffi libffi/3.2 (default) A portable foreign-function interface library
libgmp libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 The GNU multiple precision arithmetic library
libmatio libmatio/1.5 (default) MATLAB MAT file I/O library
libpng libpng/1.2 (default), libpng/1.5 Reference library for supporting the Portable Network Graphics (PNG) format.
lua lua/5.3.3 (default) Lua is a powerful, efficient, lightweight, embeddable scripting language
m4 m4/1.4.18 (default) Implementation of the traditional Unix macro processor.
mathematica mathematica/10.2, mathematica/11.2, mathematica/11.3, mathematica/12.0 (default) symbolic mathematical software
Matlab matlab/2011b, matlab/2012b, matlab/2014b, matlab/2016a, matlab/2016b, matlab/2017b (default), matlab/2018b high level language and interactive environment for numerical computation, visualization, and programming
Metis metis/5.1 (default) Serial Graph Partitioning and Fill-reducing Matrix Ordering
Node.js node/6.11.3 (default), node/8.4.0 framework for building network applications
php php/7.0 (default) general-purpose scripting language for web development
Python 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, python/3.6.1+intel-16.0, python/3.7.0 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/4.8, qt/5.7 (default) cross-platform application framework
racket racket/6.7 (default) full-spectrum programming language
ARM (former Allinea) performance reports reports/18.0.1 (default) profiler
rstudio rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) Open source edition of RStudio, an integrated development environment (IDE) for R.
scilab scilab/5.5 (default) environment for numerical computation
scons scons/2.5.1 (default), scons/3.0.0 Open source software construction tool expanding on Make and autoconf/automake.
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/110.79, smlnj/110.80 (default), smlnj/110.85 compiler for the Standard ML ‘97 programming language
subversion subversion/1.9.4 (default) Version control
Valgrind valgrind/3.12+gcc-6.2 (default) Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.
yasm yasm/1.3.0 (default) The Yasm Modular Assembler Project

differentiation

Application Version Description
JAX jax/0.1.39 (default) Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more

disk

Application Version Description
xdiskusage xdiskusage/1.51 (default) Graphical display of disk usage

docs

Application Version Description
doxygen doxygen/1.8 (default) Doxygen is a JavaDoc like documentation system for C++, C, Java and IDL.
flex 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, texinfo/6.3 (default) GNU documentation system

documentation

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

electronic structure

Application Version Description
pyscf pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 Python Module for Quantum Chemistry

evolution

Application Version Description
SLiM SLiM/2.4, SLiM/3.0 (default) Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.
breseq breseq/0.32.0 (default) Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes.

general programming

Application Version Description
R R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default) The R language and environment for statistical computing and graphics.
haskell-stack haskell-stack/1.1 (default) cross-platform program for developing Haskell projects
IDL idl/8.2 (default) scientific programming language for visualization
java java/1.7, java/1.8 (default), java/11.0.1 programming language
julia julia/0.4, julia/0.5, julia/0.5+intel-16.0, julia/0.6, julia/0.6.2, julia/1.0.1, julia/1.1.0 (default) The Julia dynamic programming language for technical computing.
libffi libffi/3.2 (default) A portable foreign-function interface library
libgmp libgmp/4.3.1, libgmp/6.1 (default), libgmp/6.1.0+gcc-6.2 The GNU multiple precision arithmetic library
libmatio libmatio/1.5 (default) MATLAB MAT file I/O library
libpng libpng/1.2 (default), libpng/1.5 Reference library for supporting the Portable Network Graphics (PNG) format.
Matlab matlab/2011b, matlab/2012b, matlab/2014b, matlab/2016a, matlab/2016b, matlab/2017b (default), matlab/2018b high level language and interactive environment for numerical computation, visualization, and programming
Node.js node/6.11.3 (default), node/8.4.0 framework for building network applications
php php/7.0 (default) general-purpose scripting language for web development
Python 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, python/3.6.1+intel-16.0, python/3.7.0 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/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) Open source edition of RStudio, an integrated development environment (IDE) for R.
SML/NJ smlnj/110.79, smlnj/110.80 (default), smlnj/110.85 compiler for the Standard ML ‘97 programming language
stata stata/14, stata/15 (default) General-purpose statistical software package developed by StataCorp.
vtune vtune/2017 (default), vtune/2018, vtune/2019 Intel Vtune Profiler developed by Intel Corp.

genetics

Application Version Description
MACS MACS/1.4 (default) Model-based Analysis for ChIP-Seq
MEME MEME/4.11 (default) Motif-based sequence analysis tools.
RSEM RSEM/1.3 (default) Accurate quantification of gene and isoform expression from RNA-Seq data.
SLiM SLiM/2.4, SLiM/3.0 (default) Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.
bcftools bcftools/1.4.1 (default) BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools.
bcl2fastq2 bcl2fastq2/2.20 (default) Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.
blast blast/2.9.0 (default) BLAST+: command-line tools for Basic Local Alignment Search
bowtie bowtie/1.1.2, bowtie/1.2.1.1 (default) DNA sequence alignment software
bowtie2 bowtie2/2.2.9 (default) DNA sequence alignment software
breseq breseq/0.32.0 (default) Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes.
bwa bwa/0.7.15 (default) Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
cellranger cellranger/2.1.1 (default), cellranger/3.0.0 An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats.
cufflinks cufflinks/2.2 (default) Transcriptome assembly and differential expression analysis for RNA-Seq.
fastqc fastqc/0.11.5 (default) A quality control tool for high throughput sequence data.
fastx_toolkit fastx_toolkit/0.0 (default) A collection of command-line tools for FASTA sequence files preprocessing
gatk gatk/3.7 (default) Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data
gcta gcta/1.91.2, gcta/1.92.2 (default) Software for genome-wide complex trait analysis.
gemma gemma/0.98 (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).
htslib htslib/1.4.1 (default) C library for high-throughput sequencing data formats; originally distributed with samtools.
picard picard/2.18.15 (default), picard/2.18.2 A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
pplacer pplacer/1.1.alpha19 (default) genetics
samtools samtools/1.2, samtools/1.4.1, samtools/1.9 (default) Tools written in C using htslib for manipulating next-generation sequencing data.
sickle sickle/1.33 (default) A windowed adaptive trimming tool for FASTQ files using quality
tophat tophat/2.1 (default) splice junction mapper for RNA-Seq reads
trinity 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 Version Description
bcl2fastq bcl2fastq/2.19.1 (default), bcl2fastq/2.20 Demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
BEAGLE beagle/trunk (default) library for core calculations with phylogenetics packages
BEAST beast/1.8 (default) Bayesian analysis of molecular sequences
plink plink/1.07, plink/1.90, plink/1.90b6.9 (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.
trinity trinity/2.2 (default) a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
vcftools 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.

genomics

Application Version Description
HISAT HISAT/2.1.0 (default) Fast and sensitive alignment program for mapping next-generation sequencing reads to a population of human genomes
MACS MACS/1.4 (default) Model-based Analysis for ChIP-Seq
MEME MEME/4.11 (default) Motif-based sequence analysis tools.
RSEM RSEM/1.3 (default) Accurate quantification of gene and isoform expression from RNA-Seq data.
SLiM SLiM/2.4, SLiM/3.0 (default) Selection on Linked Mutations (SLiM): A forward population genetic simulation for studying linkage effects, such as hitchhiking, background selection, and Hill-Robertson interference.
STAR STAR/2.6.1b (default) Spliced Transcripts Alignment to a Reference
bcftools bcftools/1.4.1 (default) BCFtools are meant as a faster replacement for most of the perl vcftools commands; originally distributed with samtools.
bcl2fastq2 bcl2fastq2/2.20 (default) Sequencing software used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis.
blast blast/2.9.0 (default) BLAST+: command-line tools for Basic Local Alignment Search
bowtie bowtie/1.1.2, bowtie/1.2.1.1 (default) DNA sequence alignment software
breseq breseq/0.32.0 (default) Computational pipeline for identfying mutations in short-read DNA re-sequencing data for haploid microbial genomes.
bs-cli bs-cli/0.9.17 (default) BaseSpace Sequence Hub CLI
bwa bwa/0.7.15 (default) Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
cellranger cellranger/2.1.1 (default), cellranger/3.0.0 An analysis pipeline for processing Chromium single-cell RNA-sequences. Capable of converting BCL files from Illumina sequencing systems to FASTQ file formats.
gatk gatk/3.7 (default) Genome Analysis Toolkit: variant siscovery in high-throughput sequencing data
gcta gcta/1.91.2, gcta/1.92.2 (default) Software for genome-wide complex trait analysis.
gemma gemma/0.98 (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).
htslib htslib/1.4.1 (default) C library for high-throughput sequencing data formats; originally distributed with samtools.
Integrative Genomics Viewer Tools igv/2.4.11 (default) A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Integrative Genomics Viewer Tools igvtools/2.3.98 (default) Accompanying CLI tools for IGV
interproscan interproscan/5 (default) Software package that allows sequences (protein and nucleic) to be scanned against InterPro’s signatures
picard picard/2.18.15 (default), picard/2.18.2 A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
redundans redundans/0.13c (default) Redundans takes as input assembled contigs, sequencing libraries and/or reference sequence and returns scaffolded homozygous genome assembly.
samtools samtools/1.2, samtools/1.4.1, samtools/1.9 (default) Tools written in C using htslib for manipulating next-generation sequencing data.
tophat tophat/2.1 (default) splice junction mapper for RNA-Seq reads

geoscience

Application Version Description
Geometry Engine - Open Source (GEOS) geos/3.6 (default), geos/3.7.0 spatial predicates and functions for processing geometry
UDUNITS udunits/2.2 (default) support package for units of physical quantities

gis

Application Version Description
postgis postgis/2.3, postgis/2.3.2+gcc-6.2 (default) PostGIS is a spatial database extender for PostgreSQL object-relational database

graphical interfaces

Application Version Description
Qt qt/4.8, qt/5.7 (default) cross-platform application framework

graphics

Application Version Description
R R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default) The R language and environment for statistical computing and graphics.
Persistence of Vision Raytracer povray/3.7 (default) Ray tracing tool for creating three-dimensional graphics.
rstudio rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) Open source edition of RStudio, an integrated development environment (IDE) for R.

graphs

Application Version Description
mcl mcl/14.137 (default) Markov Cluster Algorithm

high energy physics

Application Version Description
Class Library for High Energy Physics (CLHEP) clhep/2.3 (default) C++ mathematical library for high energy physics analysis
Fermi Science Tools fermi-fssc/v10r0p5 (default) suite of tools for the analysis of both LAT and GBM data
geant4 geant4/10.01 (default), geant4/10.02.p03, geant4/10.03.p02 a toolkit for the simulation of particles through matter

image

Application Version Description
ImageMagick ImageMagick/7.0.7-3 (default) ImageMagick can create, edit, compose, or convert bitmap images.
libjpeg-turbo libjpeg-turbo/1.5.2+gcc-6.2 (default) libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression
libjpeg-turbo libjpeg-turbo8/8d (default) libjpeg-turbo8 from IJG

image processing

Application Version Description
afni afni/16.2, afni/18.0 (default), afni/19.0 AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.
fsl fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default) FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

image progressing

Application Version Description
spm spm/12 (default) SPM software for analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG and MEG).

imaging

Application Version Description
dicom3tools dicom3tools/1 (default) command line utilities for creating, modifying, dumping, and validating files of DICOM attributes
gate gate/8.0 (default) Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy

integration

Application Version Description
cuba cuba/git (default) library for multidimensional numerical integration

jpeg

Application Version Description
libjpeg-turbo libjpeg-turbo/1.5.2+gcc-6.2 (default) libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression
libjpeg-turbo libjpeg-turbo8/8d (default) libjpeg-turbo8 from IJG

library

Application Version Description
SuperLU_dist SuperLU_dist/5.4.0+intelmpi-5.1+intel-16.0 (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, cfitsio/3+gcc-6.2 (default), cfitsio/3.450 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
cfitsio flask/git (default) CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.
fltk fltk/1.3.4 (default) FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X
gsl 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, gsl/2.5 The GNU scientific library
lapack lapack/3.6.1 (default) Linear Algebra PACKage
Metis metis/5.1 (default) Serial Graph Partitioning and Fill-reducing Matrix Ordering
parmetis 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

linear algebra

Application Version Description
SuiteSparse SuiteSparse/4.5.5 (default), SuiteSparse/5.3.0+intel-18.0 SuiteSparse is a suite of sparse matrix algorithms

linguistics

Application Version Description
mecab mecab/0.996 (default) open source morphological analysis engine
mecab-ipadic mecab-ipadic/2.7.0 (default) open source morphological analysis engine dictionary
praat praat/5.3.42 (default) Praat: doing phonetics by computer

machine learning

Application Version Description
darknet darknet/latest (default) Open Source Neural Networks in C
mcl mcl/14.137 (default) Markov Cluster Algorithm

many-body perturbation theory

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

materials

Application Version Description
Atomic Simulation Environment (ASE) ase/3.16 (default) ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
BerkeleyGW berkeleygw/1.2.0+intelmpi-5.1+intel-16.0 (default), berkeleygw/1.2.0+openmpi-2.0+intel-16.0 software package for the evaluation of quasiparticle properties and optical responses of materials and molecules
Quantum ESPRESSO 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, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 Suite of codes for electronic-structure calculations and nanoscale materials modeling
Jmol jmol/14.29 (default) molecular viewer and editor
Pathways Program in Molecular Engineering Env settings ppme/1.0 (default) Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering
pyscf pyscf/1.2.1 (default), pyscf/1.6.1+python-3.5.2+intel-16.0 Python Module for Quantum Chemistry

materials science

Application Version Description
avogadro avogadro/1.2.0 (default) Molecule editor and visualization tool
mkl/2017 dftbplus/18.1+intelmpi-2017.up4+intel-17.0 (default) Density Functional based Tight Binding (DFTB) method

math library

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

mathematics

Application Version Description
bertini bertini/1.5.1 (default), bertini/1.5.1+openmpi-2.0.2+gcc-6.2 a general-purpose solver, written in C, that was created for research about polynomial continuation
macaulay2 macaulay2/1.6 (default), macaulay2/1.8 software system devoted to supporting research in algebraic geometry and commutative algebra
mathematica mathematica/10.2, mathematica/11.2, mathematica/11.3, mathematica/12.0 (default) symbolic mathematical software

matrix computation

Application Version Description
arpack arpack/3.5.0 (default) Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.

media

Application Version Description
blender blender/2.78a (default) Blender is the free and open source 3D creation suite
ffmpeg ffmpeg/3.2 (default), ffmpeg/3.3 A complete, cross-platform solution to record, convert and stream audio and video.
mplayer mplayer/1.3.0 (default) Movie player
tiff tiff/4.0.6 (default) LibTIFF - TIFF Library and Utilities
vpx vpx/1.6 (default)  
x264 x264/0.148 (default) x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
x265 x265/2.1 (default) x265

medical

Application Version Description
slicer slicer/4.5.0 (default), slicer/4.8.1 software platform for the analysis and visualization of medical images and research in image guided therapy

medicine

Application Version Description
dicom3tools dicom3tools/1 (default) command line utilities for creating, modifying, dumping, and validating files of DICOM attributes

messaging

Application Version Description
rabbitmq rabbitmq/3.7.15 (default) message broker

molecular dynamics

Application Version Description
Atomic Simulation Environment (ASE) ase/3.16 (default) ASE is an Atomic Simulation Environment written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations.
avogadro avogadro/1.2.0 (default) Molecule editor and visualization tool
DeePMD deepmd/0.12.4 (default) Package for building deep learning based models of interatomic potential energy and force field
Quantum ESPRESSO 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, espresso/6.1-west-3.1.0+intelmpi-2017.up4+intel-17.0, espresso/6.1-west-3.1.0+intelmpi-2018.2.199+intel-18.0, espresso/6.2.1+intelmpi-2018.2.199+intel-18.0, espresso/6.4+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0 Suite of codes for electronic-structure calculations and nanoscale materials modeling
Gaussian gaussian/09RevA.02, gaussian/09RevB.01 (default), gaussian/09RevD.01, gaussian/16RevA.03 electronic structure and quantum chemistry
HOOMD-blue hoomd/2.3.0 (default) HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
i-pi i-pi/2.0 (default) A Universal Force Engine for Advanced Molecular Dynamics
openbabel openbabel/2.3 (default), openbabel/2.4 toolbox for using chemical data
openbabel openbabel_nopy/2.3 (default) toolbox for using chemical data
Orca orca/3.0 (default), orca/4.0, orca/4.1 Quantum Chemistry Electronic Structure Package
Pathways Program in Molecular Engineering Env settings ppme/1.0 (default) Setup environment to find required software and utilities for the Pathways Program in Molecular Engineering
qbox qbox/1.66.2+intelmpi-5.1+intel-16.0, qbox/1.66.3+intelmpi-2018.2.199+intel-18.0 (default), qbox/1.67.3+intelmpi-2018.2.199+intel-18.0 scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism

molecular visualization

Application Version Description
avogadro avogadro/1.2.0 (default) Molecule editor and visualization tool

multimedia

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

network

Application Version Description
netcat netcat/1.10 (default) Computer networking utility for reading from and writing to network connections using TCP or UDP

network library

Application Version Description
libfabric libfabric/1.7.0 (default) Open Fabrics Interfaces (OFI) is a framework focused on exporting fabric communication services to applications

neural networks

Application Version Description
darknet darknet/latest (default) Open Source Neural Networks in C

neuroscience

Application Version Description
afni afni/16.2, afni/18.0 (default), afni/19.0 AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.
fsl fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default) FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
spm spm/12 (default) SPM software for analysis of brain imaging data sequences (fMRI, PET, SPECT, EEG and MEG).

numerical

Application Version Description
cuba cuba/git (default) library for multidimensional numerical integration

numerical analysis

Application Version Description
MINUIT2 Minuit2/5.34 (default) library for function minimization
Armadillo armadillo/7.5 (default), armadillo/7.6, armadillo/7.8 C++ linear algebra software library
arpack arpack/3.5.0 (default) Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
Class Library for High Energy Physics (CLHEP) clhep/2.3 (default) C++ mathematical library for high energy physics analysis
eigen eigen/3.2 (default) C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
JAX jax/0.1.39 (default) Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
Intel Math Kernel Library (MKL) mkl/10.3, mkl/11.2, mkl/11.3, mkl/2017 (default), mkl/2017.up4, mkl/2018.up2, mkl/2019.up1 library of optimized numerical routines
openblas openblas/0.2.19 (default), openblas/0.3.1 Optimized BLAS library based on GotoBLAS2 1.13 BSD version. .

optimization

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

parallel

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

parser

Application Version Description
antlr antlr/2.7.7 (default) ANother Tool for Language Recognition

paste

Application Version Description
xclip xclip/latest+gcc-6.2 (default) xclip provides an interface to X selections from the command line
xsel xsel/latest+gcc-6.2 (default) XSel is a command-line program for getting and setting the contents of the X selection

physics

Application Version Description
harminv harminv/1.4 (default) A free program (and accompanying library) to solve the problem of harmonic inversion.
meep meep/1.16+intelmpi-5.1+intel-16.0 (default) A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.

postgres

Application Version Description
postgis postgis/2.3, postgis/2.3.2+gcc-6.2 (default) PostGIS is a spatial database extender for PostgreSQL object-relational database

profiler

Application Version Description
oprofile oprofile/1.2.0+gcc-7.2.0 (default) profiler

profiling

Application Version Description
ARM (former Allinea) forge (ddt, map) forge/18.0.1 (default) debugger and profiler
ARM (former Allinea) performance reports reports/18.0.1 (default) profiler

programming

Application Version Description
elixir elixir/1.9.0 (default) A dynamic, functional language designed for building scalable and maintainable applications.
make make/4.0 (default) GNU Make utility

proteins

Application Version Description
openbabel openbabel/2.3 (default), openbabel/2.4 toolbox for using chemical data
openbabel openbabel_nopy/2.3 (default) toolbox for using chemical data

python

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

simulation

Application Version Description
comsol comsol/53a, comsol/54 (default), comsol/54trial physics simulations
gate gate/8.0 (default) Simulations of Preclinical and Clinical Scans in Emission Tomography, Transmission Tomography and Radiation Therapy
geant4 geant4/10.01 (default), geant4/10.02.p03, geant4/10.03.p02 a toolkit for the simulation of particles through matter
HOOMD-blue hoomd/2.3.0 (default) HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
libctl libctl/4.1.3 (default) A Guile-based library implementing flexible control files for scientific simulations.
LUMERICAL lumerical/2016a, lumerical/2017b (default) Photonic Component & Circuit Design Software
meep meep/1.16+intelmpi-5.1+intel-16.0 (default) A finite-difference time-domain (FDTD) simulation software package to model electromagnetic systems.
wannier90 wannier90/3.0 (default) Maximally localized Wannier functions.

slrum

Application Version Description
swarm swarm/latest (default) Swarm reads a list of command lines then submits all command scripts to the cluster as a Slurm job array

software

Application Version Description
google_depot_tools google_depot_tools/1.0 (default) Google Tools for working with Chromium development

statistics

Application Version Description
MultiNest MultiNest/git (default) Nested Sampling Monte Carlo library
R R/2.15, R/3.0, R/3.2, R/3.3, R/3.3+intel-16.0, R/3.4, R/3.4.1, R/3.4.3, R/3.5.1, R/3.6.1 (default) The R language and environment for statistical computing and graphics.
BEAGLE beagle/trunk (default) library for core calculations with phylogenetics packages
jags 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.
rstudio rstudio/1.1.138, rstudio/1.1.383, rstudio/1.1.453, rstudio/1.1.9, rstudio/1.2.1335 (default) Open source edition of RStudio, an integrated development environment (IDE) for R.
sas sas/9.4 (default) business intelligence software
stata stata/14, stata/15 (default) General-purpose statistical software package developed by StataCorp.

system

Application Version Description
proot proot/current (default) user-space implementation of chroot, mount –bind, and binfmt_misc

systems research

Application Version Description
gem5 gem5/2015-09-03 (default) Modular platform for computer-system architecture research, encompassing system-level architecture as well as processor microarchitecture.

terminal

Application Version Description
tmux tmux/current (default) tmux is a terminal multiplexer, it enables a number of terminals (or windows) to be accessed and controlled from a single terminal.

testing

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

text

Application Version Description
pandoc pandoc/1.13 (default) Document converter supporting many markup formats
tkdiff tkdiff/4.2 (default) graphical interface for diff
xpdf xpdf/3.04 (default) pdf viewer and utilities

text editor

Application Version Description
GNU Emacs emacs/25 (default) GNU Emacs text editor
vim vim/7.4 (default) advanced text editor

typesetting

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

usage

Application Version Description
xdiskusage xdiskusage/1.51 (default) Graphical display of disk usage

utility

Application Version Description
lftp lftp/4.8.4 (default) file transfer program for CLI

version control

Application Version Description
git git/2.10 (default) distributed version control system
git-lfs git-lfs/1.4 (default) an open source git extension for versioning large files
Mercurial mercurial/4.0 (default) distributed version control system

video

Application Version Description
blender blender/2.78a (default) Blender is the free and open source 3D creation suite
ffmpeg ffmpeg/3.2 (default), ffmpeg/3.3 A complete, cross-platform solution to record, convert and stream audio and video.
mplayer mplayer/1.3.0 (default) Movie player
vpx vpx/1.6 (default)  
x264 x264/0.148 (default) x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
x265 x265/2.1 (default) x265

visualization

Application Version Description
MapRes 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).
ferret 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
fv fv/5.4 (default) Fv is the easy to use graphical program for viewing and editing any FITS format image or table.
Gephi gephi/0.9 (default) visualization and exploration of network data
IDL idl/8.2 (default) scientific programming language for visualization
opencv opencv/2.4 (default), opencv/3.1 Open Source Computer Vision library
pgplot pgplot/5.2 (default) Fortran- or C-callable, device-independent graphics package for making simple scientific graphs
Persistence of Vision Raytracer povray/3.7 (default) Ray tracing tool for creating three-dimensional graphics.
Teem teem/trunk (default) scientific raster data visualization
vmd vmd/1.9.2 (default) molecular visualization program
vtk vtk/7.0 (default), vtk/7.1+python-2.7.12 The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing, and visualization.

workflow

Application Version Description
AiiDA aiida/1.0.0b3 (default) Workflow tool for Computational Science