Materials Modeling and Electronic Structure Calculations

Amsterdam Density Functional

A program suite for small-angle scattering data analysis from biological macromolecules

A Computational Chemistry program for Molecular Modeling and Simulation

Molecular modeling system

Software computing electronic wave function and properties of periodic systems

Simulation Software for Molecular Dynamics

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)

An application that provides state-of-the-art capabilities for electronic structure modeling

GROMACS is a versatile package to perform molecular dynamics

Program for performing a variety of types of simulations on materials

Large-scale Atomic/Molecular Massively Parallel Simulator

A DFT Exchange and Correlation Functionals Library

A general text-based molecule builder for LAMMPS.

A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

The Natural Bond Orbital (NBO) program NBO 6.0 is a discovery tool for chemical insights from complex wavefunctions.

Application for high performance computational chemistry

ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties

An Open-Source Visualization Tool for VASP

A molecular visualization system on an open-source Python foundation

ASE is an Atomistic Simulation Environment written in Python

Nanoscale electronic-structure calculations and materials modeling

The Vienna Ab initio Simulation Package is a computer program for atomic scale materials modelling.

A tool for obtaining maximally-localised Wannier functions

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

ANGSD is a software for analyzing next generation sequencing data.

ANTs (Advanced Normalization Tools) is a program designed to do feature extraction on complex datasets with particular focus on images like MRI

A Program to Convert BCL Data to FASTQ Format

Beagle is a High-Performance Bayesian and Maximum Likelihood Bioinformatics Library

BEAST is a Bayesian Analysis program for Building and Analyzing Phylogenetic Trees

BEST is a Phylogenetics Program design to estimate Phylogenetic Trees

Python library for computational molecular biology.

A Low-Memory Footprint Genetic Sequence Alignment Tool

Bowtie is an ultrafast, memory-efficient short read aligner

Bowtie2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences

Software package for mapping low-divergent sequences

A Program for Alignment of Multiple Genetic or Protein Sequences

A Program for Alignment of Multiple Genetic or Protein Sequences (GUI Version of Clustal W)

Transcript assembly, differential expression, and differential regulation for RNA Sequencing

A powerful Python package for animal pose estimation

A fast D-Statistics computation program

Motif Finding by Gibbs Sampling in DNA and Protein Sequences

Searching Biological Sequence Data for Regions of Similarity

A quality control tool for high throughput sequence data.

FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.

gemBS-rs is a rewrite of the gemBS pipeline using Rust. gemBS itself is a powerful high-throughput pipeline for DNA Methylation sequencing analysis.

An Interpolated Markov Model Algorithm for Gene Finding in Microbial Genomes

A Python Package for Analysis of High-Throughput Genetic Sequence Data

A Program for Aligning Multiple Sets of Genetic Sequence Data

Aligning Multiple Genome Sequences with Large-Scale Evolutionary Events

Estimates effective population sizes and past migration rates

A Bayesian MCMC Program for Inferring Phylogenetic Models

An Ultra-Fast Alignment Program for Genomic and Protein Sequence Data

An MRI Image Registration Tool

RELION is a powerful biomacromolecular structure determination package for CryoEM applications.

Ultrafast universal RNA sequencing aligner

Flexible generic format for storing nucleotide sequence alignments

A Program for Ultrafast RNA-seq Sequence Alignments

A spliced read mapper for RNA Sequencing

A flexible read trimming tool for Illumina NGS data

VMD (Visual Molecular Dynamics) - Interactive Molecular Visualization and Analysis Software

A stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales

A cluster computing framework for large-scale data processing

GNU Autoconf is a package to automate the production of software configuration shell scripts

The client program for bbFTP, which is designed for transfer of very large files

Blender is a free and open source 3D animation suite

CDO - Command Line Tools for Climate Model Data Analysis

A Set of Tools to Simplify Building, Testing and Packaging Software

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.

A Linux Program for Decoding Raw Digital Image Files

Audio and Video Generation and Conversion Software

Partial differential equation solver based on the finite element method

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.

Solver of partial differential equations used in fluid flow.

Git - A Version Control System for Software Development

A WYSIWYG 2D plotting tool for scientific graphing

GrADS - A Data Analysis and Display System for the Earth Sciences

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.

A GUI Tool for Editing Files for the HDF4 and HDF5 Programs

An Interactive Shell for Python with Jupyter Graphical Support

A Gibbs Sampler for Bayesian Hierarchical Models with MCMC

Detailed instructions on how to set up and use Jupyter on Open OnDemand

Knight Lab Tools are a set of open-source tools developed by Northwestern University for data management, storytelling, and enhancing research through visualization.

LibreOffice is a powerful GUI application for word processing, spreadsheet calculation and database management

A Package to Dynamically Manipulate User Environments with Modules

Set of open-source software tools for creating coupled models

A Visualization Browser for netCDF Data

A graphical UNIX Text Editor

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: 

A Parallel Implementation of the K-Means Clustering Algorithm

ParaView is an open-source, multi-platform data analysis and visualization application

A Graph and Mesh Partitioning and Sparse Matrix Ordering Program

A powerful and simple tool to find and compiler options for libraries.

A popular, full featured, statistical computing package

R Studio is an integrated development environment R. It enables users to create programs using R language.

A Scientific Computing Library for Graph Partitioning and Mapping

A powerful HPC Container Solution similar to and compatible with Docker

A Powerful Open-Source Network Security Tool

SPSS is a powerful GUI statistics program built by IBM

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.

Stata is fully featured data analysis and statistical software

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.

A GUI-based parallel and serial debugging tool

Program Package For Electronic Structure Calculations

A software package for visualizing scientific results

A Program for Decoding and Working with GRIB Data Files

Algorithms and Libraries for Physics Simulations

A high quality linear algebra library (matrix maths) for the C++ language, aiming towards a good balance between speed and ease of use

A collection of Fortran77 subroutines designed to solve large scale eigenvalue problems

Linear Algebra Library

Boost - A Powerful, Multipurpose library of C++ Tools

The Data Acquisition Library for the Snort IDS

C library to compute the discrete Fourier transforms

An Automatic Basis Function Tabulator for the Finite Element Package FEniCS

A Python library to Work With Text Font Files

FMRIB Software Library

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.

An API for the HDF5 Data Format for Python

Tools and File Structures for Storing and Analyzing Scientific Data

unique technology suite that makes possible the management of large and complex data

Library for solving large, sparse linear systems of equations on massively parallel computers

Standard software library for linear algebra

An Implementation of MPI Bindings for Python

A Highly Scalable MPI Implementation for High-End Computer Systems

Libraries for representing scientific data

A Highly Optimized Linear Algebra Library based on GotoBLAS

A Powerful Library for Computer Vision Applications

An MPI Implementation for Parallel Computing

A powerful machine learning library for Python

A High-Performance Linear Algebra Library

Library for the direct solution of large, sparse, nonsymmetric systems of linear equations.

A Powerful Deep Learning Library with GPU Support

Python 2.7, 3.7 and 3.8 with 195 popular packages

A Modern Parallel Programming Language

A Front-End for LLVM-Based C Compilers

CUDA is a parallel computing platform and programming model for GPUs invented by NVIDIA.

A Static Compiler for the Python and Cython Languages

GNU C, C++, and Fortran Compilers

A high-level language, primarily intended for numerical computations

Intel C, C++, and Fortran Compilers

A High-Performance Numerical Computing Environment and Language

A Toolkit for Building Compilers

A high-level language and interactive environment for numerical computation, visualization, and programming

An Assembler for x86 Assembly Code

NVIDIA's HPC Toolkit including CUDA Fortran, NVCC, NVC++ and other tools packaged with CUDA 11.6

PGI Compilers for C, C++, and Fortran

Interactive, object-oriented, extensible programming language

A Modular Assembler code for x86 and AMD64 Assembly Code