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

JSON

Application	Version	Description
jq	jq/1.5 (default)	jq is a lightweight and flexible command-line JSON processer

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), R/3.6.3-no-openblas, R/4.0.0, R/4.0.4, R/4.1.0, R/4.1.0-no-openblas	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
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, picard/2.18.2, picard/2.21.8 (default)	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, bcftools/1.9 (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, beast/2.3 (default), beast/2.6.2	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/6.0.3, fsl/6.0.4	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), vmd/1.9.3, vmd/1.9.4	molecular visualization program

browser

Application	Version	Description
firefox	firefox/67.0 (default), firefox/91.0.1esr, firefox/esr	web browser

checkpointing

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

chemistry

Application	Version	Description
amber	amber/16, amber/16+intelmpi-2018.2.199+intel-18.0, amber/18, amber/18+intelmpi-2017.up4+intel-17.0, amber/20+intelmpi-2017.up4+intel-17.0 (default)	suite of biomolecular simulation programs
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, crux/3.2.3 (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-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0, espresso/6.6+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/2.2.0 (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, orca/4.2	Quantum Chemistry Electronic Structure Package
ovito	ovito/3.0 (default)	Scientific visualization and analysis software for atomistic and particle simulation data
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
tinker	tinker/8.6 (default), tinker/8.6+intel-18.0	Software Tools for Molecular Design
wannier90	wannier90/3.0 (default)	Maximally localized Wannier functions.
XCrySDen	xcrysden/1.6 (default)	A crystalline and molecular structure visualisation program

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/10.1.0, gcc/10.2.0, gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0, gcc/9.1.0, gcc/9.2.0	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, intel/19.0.4, intel/19.1.1	C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
java	java/1.7, java/1.8 (default), java/11.0.1, java/15.0.2	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, julia/1.1.1, julia/1.4.2 (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.

computer vision

Application	Version	Description
opencv	opencv/2.4, opencv/3.1, opencv/4.0 (default)	OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Being a BSD-licensed product, OpenCV makes it easy for businesses to utilize and modify the code.

container

Application	Version	Description
singularity	singularity/3.0.1, singularity/3.4.0 (default)	Application 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

crystallography

Application	Version	Description
Precognition	precognition/5.2.2 (default)	Software for processing single crystal diffraction images and yields experimentally-observed structure factor amplitudes.

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), curl/7.75.0	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, hdf5/1.10.7+intelmpi-2018.2.199+intel-18.0, hdf5/1.12.0+openmpi-4.0+pgi-2017, hdf5/1.12.0+pgi-2017, 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, netcdf/4.7.4-c-cxx-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, ROOT/6.22.02+gcc-10.1.0	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/4.3.0+gcc-10.2.0	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, hdf5/1.10.7+intelmpi-2018.2.199+intel-18.0, hdf5/1.12.0+openmpi-4.0+pgi-2017, hdf5/1.12.0+pgi-2017, 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
artifice	artifice/0.0 (default)	Object detection for scientific images
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
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), R/3.6.3-no-openblas, R/4.0.0, R/4.0.4, R/4.1.0, R/4.1.0-no-openblas	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
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/1.55, 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, boost/1.73.0-CXX14+gcc-10.1.0	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/3.15, cmake/3.6.2	Cross-platform build system.
Nvidia CUDA Toolkit	cuda/10.0, cuda/10.1, cuda/11.0, cuda/11.2, cuda/6.5 (default), cuda/7.5, cuda/8.0, cuda/9.0, cuda/9.0a, cuda/9.1, cuda/9.2	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/10.1.0, gcc/10.2.0, gcc/4.4.7, gcc/6.1 (default), gcc/6.2, gcc/6.3.0, gcc/7.2.0, gcc/8.2.0, gcc/9.1.0, gcc/9.2.0	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+gcc-7.2.0, 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, intel/19.0.4, intel/19.1.1	C/C++/Fortran compiler suite, including Intel Threaded-Building-Blocks
java	java/1.7, java/1.8 (default), java/11.0.1, java/15.0.2	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, julia/1.1.1, julia/1.4.2 (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
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/anaconda-2019.03, python/anaconda-2020.02 (default), python/anaconda-2021.05, python/cpython-3.7.0, python/cpython-3.8.5, python/intel-2020.up1	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

differential solvers

Application	Version	Description
Hypre	hypre/2.17 (default)	A library of high performance preconditioners and solvers featuring multigrid methods for the solution of large, sparse linear systems of equations on massively parallel computers

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.)

economics

Application	Version	Description
dynare	dynare/4.5 (default)	Software platform for handling a wide class of economic models.

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), R/3.6.3-no-openblas, R/4.0.0, R/4.0.4, R/4.1.0, R/4.1.0-no-openblas	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, java/15.0.2	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, julia/1.1.1, julia/1.4.2 (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.
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/anaconda-2019.03, python/anaconda-2020.02 (default), python/anaconda-2021.05, python/cpython-3.7.0, python/cpython-3.8.5, python/intel-2020.up1	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, stata/16 (default)	General-purpose statistical software package developed by StataCorp.
vtune	vtune/2017 (default), vtune/2018, vtune/2019, vtune/2020	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, bcftools/1.9 (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, picard/2.18.2, picard/2.21.8 (default)	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, beast/2.3 (default), beast/2.6.2	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), STAR/2.7.7a	Spliced Transcripts Alignment to a Reference
bcftools	bcftools/1.4.1, bcftools/1.9 (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.
bwa	bwa/0.7.15 (default)	Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
canu	canu/2.1 (default)	Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
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.
fasta	fasta/36.3 (default)	protein and DNA sequence similarity searching and alignment programs
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, picard/2.18.2, picard/2.21.8 (default)	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), R/3.6.3-no-openblas, R/4.0.0, R/4.0.4, R/4.1.0, R/4.1.0-no-openblas	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, geant4/10.06.p03, geant4/10.7.0	a toolkit for the simulation of particles through matter

high performance computing

Application	Version	Description
Intel MPI Library	intelmpi/2017.up4+intel-17.0, intelmpi/2018.2.199+intel-18.0, intelmpi/2018.4.274+intel-18.0.5, intelmpi/2019.up7+intel-19.1.1, intelmpi/4.0+intel-12.1, intelmpi/5.0+intel-15.0, intelmpi/5.1+intel-16.0 (default)	MPI library
OpenMPI	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, openmpi/2.0.2+gcc-6.2, openmpi/3.0.0, openmpi/3.0.0+gcc-10.1.0, openmpi/3.0.0+gcc-6.2, openmpi/3.0.0+gcc-7.2.0, openmpi/3.1.2, openmpi/4.0+pgi-2017	A High Performance Message Passing Library

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 analysis

Application	Version	Description
artifice	artifice/0.0 (default)	Object detection for scientific images

image processing

Application	Version	Description
afni	afni/16.2, afni/18.0 (default), afni/19.0, afni/21.0	AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data.
Convert3D	c3d/1.1 (default)	A command-line tool for converting 3D images between common file formats
cisTEM	cistem/1.0.0-beta (default)	cisTEM is a computational imaging system for transmission electron microscopy
fsl	fsl/5.0.11, fsl/5.0.9, fsl/6.0.0, fsl/6.0.1 (default), fsl/6.0.3, fsl/6.0.4	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+gcc-7.2.0, 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
Simple DirectMedia Layer (SDL)	libsdl/1.2 (default)	A cross-platform development library designed to provide low level access to audio, keyboard, mouse, joystick, and graphics hardware via OpenGL and Direct3D
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
spfft	spfft/0.9.8+openmpi-3.0.0+gcc-10.1.0 (default)	SpFFT - A 3D FFT library for sparse frequency domain data written in C++
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-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0, espresso/6.6+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
ovito	ovito/3.0 (default)	Scientific visualization and analysis software for atomistic and particle simulation data
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
XCrySDen	xcrysden/1.6 (default)	A crystalline and molecular structure visualisation program

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, elpa/2017.11.001+intelmpi-2018.2.199+intel-18.0 (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
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), arpack/3.7.0+intelmpi-2017.up4+intel-17.0	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/4.10.2, slicer/4.11, 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
amber	amber/16, amber/16+intelmpi-2018.2.199+intel-18.0, amber/18, amber/18+intelmpi-2017.up4+intel-17.0, amber/20+intelmpi-2017.up4+intel-17.0 (default)	suite of biomolecular simulation programs
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-elpa-2017.11+intelmpi-2018.2.199+intel-18.0, espresso/6.4-environ-1.1+intelmpi-2018.2.199+intel-18.0, espresso/6.6+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/2.2.0 (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, orca/4.2	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, qbox/1.71.4+intelmpi-2018.2.199+intel-18.0	scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism
XCrySDen	xcrysden/1.6 (default)	A crystalline and molecular structure visualisation program

molecular modeling

Application	Version	Description
tinker	tinker/8.6 (default), tinker/8.6+intel-18.0	Software Tools for Molecular Design

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/21.0	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/6.0.3, fsl/6.0.4	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), arpack/3.7.0+intelmpi-2017.up4+intel-17.0	Collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.
artifice	artifice/0.0 (default)	Object detection for scientific images
Class Library for High Energy Physics (CLHEP)	clhep/2.3 (default)	C++ mathematical library for high energy physics analysis
eigen	eigen/3.2 (default), eigen/3.3	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, mkl/2019.up4, mkl/2020.up1	library of optimized numerical routines
openblas	openblas/0.2.19 (default), openblas/0.3.1, openblas/0.3.13	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
jq	jq/1.5 (default)	jq is a lightweight and flexible command-line JSON processer

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

photonic

Application	Version	Description
lumerical	lumerical/2016a, lumerical/2017b, lumerical/2020a (default)	Photonic Component & Circuit Design Software

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.
ovito	ovito/3.0 (default)	Scientific visualization and analysis software for atomistic and particle simulation data

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.
gperf	gperf/3.1 (default)	GNU perfect hash function generator
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, comsol/54trial, comsol/55, comsol/56 (default)	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, geant4/10.06.p03, geant4/10.7.0	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, lumerical/2020a (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), R/3.6.3-no-openblas, R/4.0.0, R/4.0.4, R/4.1.0, R/4.1.0-no-openblas	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/4.3.0+gcc-10.2.0	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, stata/16 (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/3.1c, 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), pandoc/2.9.2.1	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, emacs/26 (default)	GNU Emacs 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
ovito	ovito/3.0 (default)	Scientific visualization and analysis software for atomistic and particle simulation data
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), vmd/1.9.3, vmd/1.9.4	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.
XCrySDen	xcrysden/1.6 (default)	A crystalline and molecular structure visualisation program

workflow

Application	Version	Description
AiiDA	aiida/1.0.0b3 (default), aiida/1.2.1	Workflow tool for Computational Science