Software Library
This inventory includes major software packages available on our compute systems. If you would like us to install a package not listed here, please let us know.
Available Software
ABINIT | 9.4.1 | Materials Modeling and Electronic Structure Calculations |
ADF | 2016.101 | Amsterdam Density Functional |
atsas | 3.0.3 | A program suite for small-angle scattering data analysis from biological macromolecules |
Charmm | 41 | A Computational Chemistry program for Molecular Modeling and Simulation |
Chimera | 1.8.1 | Molecular modeling system |
Crystal17 | Crystal17/1.0.2 | Software computing electronic wave function and properties of periodic systems |
Desmond | 3.4.0.2 | Simulation Software for Molecular Dynamics |
FPLO | 22.00-62 | The FPLO® package is a full-potential local-orbital code to solve the Kohn-Sham equations on a regular lattice or with free boundary conditions (finite systems) |
Gaussian | v16 | An application that provides state-of-the-art capabilities for electronic structure modeling |
GROMACS | 2021.2 | GROMACS is a versatile package to perform molecular dynamics |
GULP | 6.0 | Program for performing a variety of types of simulations on materials |
LAMMPS | 20201029 | Large-scale Atomic/Molecular Massively Parallel Simulator |
libxc | 4.3.0 | A DFT Exchange and Correlation Functionals Library |
moltemplate | 2.1.2 | A general text-based molecule builder for LAMMPS. |
NAMD | 2.14 | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. |
nbo6 | 6.0 | The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions. |
NWChem | 7.0.2 | Application for high performance computational chemistry |
ORCA | 5.0.1; 4.1.2 | ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties |
P4VASP | 0.3.30 | An Open-Source Visualization Tool for VASP |
PyMOL | 2.5.0 | A molecular visualization system on an open-source Python foundation |
python-ase | 3.19.1 | ASE is an Atomistic Simulation Environment written in Python |
Quantum ESPRESSO | 6.5 | Nanoscale electronic-structure calculations and materials modeling |
VASP | 5.4.1;5.4.4 | The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling. |
wannier90 | 3.0.0 | A tool for obtaining maximally-localised Wannier functions |
ABySS | 2.1.5 | Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler |
ANGSD | 0.935 | ANGSD is a software for analyzing next generation sequencing data. |
ANTs | 2.3.5 | ANTs (Advanced Normalization Tools) is a program designed to do feature extraction on complex datasets with particular focus on images like MRI |
bcl2fastq | 2.20.0.422 | A Program to Convert BCL Data to FASTQ Format |
Beagle | 2.1 | Beagle is a High-Performance Bayesian and Maximum Likelihood Bioinformatics Library |
BEAST | 1.10.4 | BEAST is a Bayesian Analysis program for Building and Analyzing Phylogenetic Trees |
BEST | 3.1.2 | BEST is a Phylogenetics Program design to estimate Phylogenetic Trees |
Biopython | 1.79 | Python library for computational molecular biology. |
BLAT | 34 | A Low-Memory Footprint Genetic Sequence Alignment Tool |
Bowtie | 1.0.1 | Bowtie is an ultrafast, memory-efficient short read aligner |
Bowtie2 | 2.4.1. | Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences |
BWA | 0.7.17 | Software package for mapping low-divergent sequences |
Clustal W | 2.1 | A Program for Alignment of Multiple Genetic or Protein Sequences |
Clustal X | 2.1 | A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W) |
Cufflinks | 2.1.1 | Transcript assembly, differential expression, and differential regulation for RNA Sequencing |
DeepLabCut | User-Installed | A powerful Python package for animal pose estimation |
DSuite | 1.0.0 | A fast D-Statistics computation program |
ELPH | 0.1.5 | Motif Finding by Gibbs Sampling in DNA and Protein Sequences |
FASTA | 36.3.8e | Searching Biological Sequence Data for Regions of Similarity |
FASTQC | 0.11.8 | A quality control tool for high throughput sequence data. |
FreeSurfer | 7.1.1, 6.0.0 | FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. |
gemBS-rs | 4.0.0 | gemBS-rs is a rewrite of the gemBS pipeline using Rust. gemBS itself is a powerful high-throughput pipeline for DNA Methylation sequencing analysis. |
Glimmer | 3.02b | An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes |
HTSeq | 0.13.5 | A Python Package for Analysis of High-Throughput Genetic Sequence Data |
MAFFT | 7.407 | A Program for Aligning Multiple Sets of Genetic Sequence Data |
Mauve | 2.4.0 | Aligning Multiple Genome Sequences with Large-Scale Evolutionary Events |
Migrate-n | 3.6.11, 4.4.0 | Estimates effective population sizes and past migration rates |
MrBayes | 3.2.1 | A Bayesian MCMC Program for Inferring Phylogenetic Models |
MUMmer | 3.23 | An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data |
NiftyReg | 1.3.9 | An MRI Image Registration Tool |
RELION | 3.1.3 | RELION is a powerful biomacromolecular structure determination package for CryoEM applications. |
RNA-STAR | 2.4.1d | Ultrafast universal RNA sequencing aligner |
Samtools | 1.13 | Flexible generic format for storing nucleotide sequence alignments |
STAR | 2.5.3a | A Program for Ultrafast RNA-seq Sequence Alignments |
TopHat | 2.1.1 | A spliced read mapper for RNA Sequencing |
Trimmomatic | 0.36 | A flexible read trimming tool for Illumina NGS data |
VMD | 1.9.1 | VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software |
ALPS | 2.1 | Algorithms and Libraries for Physics Simulations |
Armadillo C++ Library | 9.860.2 | A high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use |
ARPACK | 3.7.0 | A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems |
BLAS | 3.2.1 | Linear Algebra Library |
Boost | 1.69.0 | Boost - A Powerful, Multipurpose library of C++ Tools |
DAQ | 2.0.6 | The Data Acquisition Library for the Snort IDS |
FFTW | 3.3.8, 2.1.5 | C library to compute the discrete Fourier transforms |
FIAT | 1.6.0.dev0 | An Automatic Basis Function Tabulator for the Finite Element Package FEniCS |
fonttools | 3.8.0 | A Python library to Work With Text Font Files |
FSL | 6.0.5, 6.0.2 | FMRIB Software Library |
GSL | 1.6, 2.3, 2.6 | The GNU Scientific Library (GSL) is a powerful library of common numerical and scientific functions intended for use in C and C++ software. It serves as an important backend in many software packages. |
h5py | 2.8.0 | An API for the HDF5 Data Format for Python |
HDF4 | 4.2.15 | Tools and File Structures for Storing and Analyzing Scientific Data |
HDF5 | 1.10.4 | unique technology suite that makes possible the management of large and complex data |
Hypre | 2.18.2 | Library for solving large, sparse linear systems of equations on massively parallel computers |
LAPACK | 3.8.0 | Standard software library for linear algebra |
MPI for Python | 3.0.0 | An Implementation of MPI Bindings for Python |
MVAPICH2 | 2.3 | A Highly Scalable MPI Implementation for High-End Computer Systems |
NetCDF | 4.8.0(gcc/intel) 4.3.1(netcdf-cxx) 4.5.3 (fortran) | Libraries for representing scientific data |
OpenBLAS | 0.3.5 | A Highly Optimized Linear Algebra Library based on GotoBLAS |
OpenCV | 3.4.6 | A Powerful Library for Computer Vision Applications |
OpenMPI | 4.1.3, 4.1.0, 2.1.0 | An MPI Implementation for Parallel Computing |
PyTorch | 1.3.1 | A powerful machine learning library for Python |
ScaLAPACK | 2.0.2 | A High-Performance Linear Algebra Library |
SuperLU | 5.4.0, 5.2.1 | Library for the direct solution of large, sparse, nonsymmetric systems of linear equations. |
TensorFlow | 2.2.0 | A Powerful Deep Learning Library with GPU Support |
Anaconda | 2.7.15, 3.7.3, 3.8.3 | Python 2.7, 3.7 and 3.8 with 195 popular packages |
Chapel | 1.13.0 | A Modern Parallel Programming Language |
Clang | 6.0.0, 7.0.1 | A Front-End for LLVM-Based C Compilers |
CUDA | 11.1 | CUDA is a parallel computing platform and programming model for GPUs invented by NVIDIA. |
Cython | 0.29.12 | A Static Compiler for the Python and Cython Languages |
GNU Compilers | 8.3.1 | GNU C, C++, and Fortran Compilers |
GNU Octave | 5.2.0 | A high-level language, primarily intended for numerical computations |
Intel Compilers | 2021.2.0 | Intel C, C++, and Fortran Compilers |
Julia | 1.6.1 | A High-Performance Numerical Computing Environment and Language |
LLVM | 6.0.0 & 3.9.1 & 7.0.1 | A Toolkit for Building Compilers |
MATLAB | 2021b, 2020a, 2018b, 2017a, 2015b | A high-level language and interactive environment for numerical computation, visualization, and programming |
NASM | 2.15.03 | An Assembler for x86 Assembly Code |
NVHPC | 22.3 | NVIDIA's HPC Toolkit including CUDA Fortran, NVCC, NVC++ and other tools packaged with CUDA 11.6 |
Portland Group Compilers | 21.3.0 64-bit | PGI Compilers for C, C++, and Fortran |
Python | 3.10.4, 3.6.8, 2.7.17 | Interactive, object-oriented, extensible programming language |
yasm | 1.3.0 | A Modular Assembler code for x86 and AMD64 Assembly Code |
Apache Spark | 2.2.1 | A cluster computing framework for large-scale data processing |
Autoconf | 2.69 | GNU Autoconf is a package to automate the production of software configuration shell scripts |
bbFTP-client | 3.2.1 | The client program for bbFTP, which is designed for transfer of very large files |
Blender | 2.69 | Blender is a free and open source 3D animation suite |
CDO | 1.9.6 | CDO - Command Line Tools for Climate Model Data Analysis |
CMake | 3.13.3 | A Set of Tools to Simplify Building, Testing and Packaging Software |
CmdSTAN | 2.30.1 | CmdSTAN is an implementation of the STAN software package for Statistical modeling. It is a powerful source-to-source compiler which compiles STAN code to C++ from which a fast and optimized executable can be generated. |
DCRAW | 9.28.0 | A Linux Program for Decoding Raw Digital Image Files |
ffmpeg | 3.1.7 | Audio and Video Generation and Conversion Software |
FreeFem++ | 4.7 | Partial differential equation solver based on the finite element method |
Gephi | 0.9 | Gephi is an open-source visualization and exploration software for graphs and networks. Its interactive structure is beneficial for several different types of data analysis. |
Gerris | 1.3.2 | Solver of partial differential equations used in fluid flow. |
Git | 2.32.0.rc2 | Git - A Version Control System for Software Development |
Grace | 5.1.25 | A WYSIWYG 2D plotting tool for scientific graphing |
GrADS | 2.0.2 | GrADS - A Data Analysis and Display System for the Earth Sciences |
HADOOP | 1.2.1 (myhadoop-0.30) | Apache Hadoop is an open-source software framework for distributed storage and distributed processing of very large data sets on computer clusters built from commodity hardware. |
HDFView | 3.0.0 | A GUI Tool for Editing Files for the HDF4 and HDF5 Programs |
IPython | 7.16.1 | An Interactive Shell for Python with Jupyter Graphical Support |
JAGS | 4.2.0 | A Gibbs Sampler for Bayesian Hierarchical Models with MCMC |
Jupyter on OpenOnDemand | N/A | Detailed instructions on how to set up and use Jupyter on Open OnDemand |
Knight Lab Tools | Knight Lab Tools are a set of open-source tools developed by Northwestern University for data management, storytelling, and enhancing research through visualization. |
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Lmod | 7.8.9 | A Package to Dynamically Manipulate User Environments with Modules |
Model Coupling Toolkit (MCT) | 2.10.0 | Set of open-source software tools for creating coupled models |
Ncview | 2.1.8 | A Visualization Browser for netCDF Data |
NEdit | 5.7 | A graphical UNIX Text Editor |
OpenRefine | 3.6 | OpenRefine previously, known as Google Refine, is a common and important tool that helps us work with big messy data in many formats. It provides the ability to clean, format, or transform thousands of records at a time with a short learning curve for its basic functionalities. It will be particularly useful for those dealing with textual data in tables supporting over 15 languages and the following formats: |
parallel-kmeans | 1 | A Parallel Implementation of the K-Means Clustering Algorithm |
ParaView | 5.5.2 | ParaView is an open-source, multi-platform data analysis and visualization application |
ParMETIS | 4.0.3 | A Graph and Mesh Partitioning and Sparse Matrix Ordering Program |
pkg-config | 1.4.2 | A powerful and simple tool to find and compiler options for libraries. |
R (statistical computing) | 4.2.0 / Several Others | A popular, full featured, statistical computing package |
R Studio | R Studio is an integrated development environment for R and Python. It enables users to create programs using R and Python languages. R Studio is available commercially and in open-source editions. |
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SCOTCH | 6.0.6 | A Scientific Computing Library for Graph Partitioning and Mapping |
Singularity (Containers) | 3.8.1 | A powerful HPC Container Solution similar to and compatible with Docker |
Snort | 2.9.7.3 | A Powerful Open-Source Network Security Tool |
SPSS | 27 | SPSS is a powerful GUI statistics program built by IBM |
Spyder | Spyder is a scientific development environment designed for and written in Python. It features advanced tools and capabilities with the visualization of a scientific package. |
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Stata | 13mp, 15, 16, 16mp | Stata is fully featured data analysis and statistical software |
Tableau | Tableau (also referred to as Tableau Public) is an open-source data visualization platform. Visualizations created with Tableau can also be made available to the public. |
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TAU | 2.23 | TAU (Tuning and Analysis Utilities) is a software performance analysis tool |
tesseract | 5.2.0 | Tesseract is an open source optical character recognition (OCR) platform. OCR extracts text from images and documents without a text layer and outputs the document into a new searchable text file, PDF, or most other popular formats. Tesseract is highly customizable and can operate using most languages, including multilingual documents and vertical text. |
TotalView | 8.13.0, 2018.2.6, 2019.2.12, 2021.3.9 | A GUI-based parallel and serial debugging tool |
TurboMole | 7.4.1 | Program Package For Electronic Structure Calculations |
VisIt | 3.0.0 | A software package for visualizing scientific results |
WGRIB | 1.8.1.2c | A Program for Decoding and Working with GRIB Data Files |