Resources software - All software

A Density Functional Theory (DFT) package, using pseudopotentials and a planewave basis.

ADIOS2 is an adaptable, scalable, and unified framework to aid scientific applications when data transfer volumes exceed the capabilities of traditional file I/O.

AI system that predicts a protein's 3D structure from its amino acid sequence.

A GPU accelerated core solver library to speed up computationally intense linear solvers

A software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).

General purpose software for mechanical engineering

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

The AutoDock Suite is a growing collection of methods for computational docking and virtual screening, for use in structure-based drug discovery and exploration of the basic mechanisms of biomolecular structure and function.

Bazel is a free software tool that allows for the automation of building and testing of software.

BCFtools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF

A toolset for genome arithmetic.

A collection of binary tools for creating and managing binary programs, object files, libraries, profile data, and assembly source code.

Basic Local Alignment Search Tool

Boost provides free peer-reviewed portable C++ source libraries.

Fast and sensitive read alignment

Cactus is a reference-free whole-genome multiple alignment program

CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format.

UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures

The bulk of the package is based on OpenCE dedicated to AI which includes (for example) Tensorflow, Pytorch, XGBoost, and other related packages and dependencies.

CMake build system

Atomistic and molecular simulations of solid state, liquid, molecular and biological systems

Crystal14 is an ab initio code that uses a Gaussian-type basis set: both pseudopotential and all-electron strategies are permitted

CTFFIND is a program for finding CTFs of electron micrographs.

The Cube 4.x series and the associated Cube4 data format is provided for Cube files produced with the Score-P performance instrumentation and measurement infrastructure, the Scalasca version 2.x trace analyzer and other compatible tools.

NVIDIA cuDNN is a GPU-accelerated library of primitives for deep neural networks

cURL is an open source command line tool and library for transferring data with URL syntax.

The Dakota project delivers both state-of-the-art research and robust, usable software for optimization and UQ.

Deal.II is a A C++ software library supporting the creation of finite element codes and an open community of users and developers.

Tools for exploring deep sequencing data

DFAST is a flexible and customizable pipeline for prokaryotic genome annotation as well as data submission to the INSDC

Dlib is a modern C++ toolkit containing machine learning algorithms and tools for creating complex software in C++ to solve real world problems.

Calculates DSSP (dictionary of protein secondary structure) entries from PDB entries

EcCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages.

 ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields.

EPIC-KITCHEN-100 dataset

Engineering and Scientific Subroutine Library

 A quality control tool for high throughput sequencing data

Fastest Fourier Transform in the West

Freebayes, a haplotype-based variant detector

Finder of somatic fusion-genes in RNA-seq data.

GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data.

Software package to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait and for other analyses of data from genome-wide association studies (GWASs)

A package for pan-genome analysis

GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating-point numbers. GMP has a rich set of functions, and the functions have a regular interface.

GMT is an open source collection of command-line tools for manipulating geographic and Cartesian data sets and producing PostScript illustrations.

A command-driven plotting program.

Grace is a WYSIWYG 2D plotting tool

GROningen Machine for Chemical Simulations - Molecular Dynamics on Parallel Computers

GNU Triangulated Surface Library

A platform for research in embodied artificial intelligence

Hierarchical Equal Area isoLatitude Pixelation of a sphere.

Horovod is a distributed deep learning training framework for TensorFlow, Keras, PyTorch, and Apache MXNet. The goal of Horovod is to make distributed deep learning fast and easy to use.

The hwloc software package provides a portable abstraction of the hierarchical topology of modern architectures

Interactive Data language

Ready-To-Use Reference Sequences and Annotations

ImageNet ILSVRC 2012 dataset

Intel MPI compilers

Development environment for building applications, applets, and components using the Java programming language.

Java Runtime Enviroment

The Jupyter notebook is a web-based notebook environment for interactive computing.

Kraken is a taxonomic sequence classifier that assigns taxonomic labels to DNA sequences.

Linear Algebra PACKage: Fortran library for solving linear equations, eigenvalue problems, and singular value problems.

 A library based on SiestaXC

 A library to handle PSML, the pseudopotential markup language

The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.

General-purpose, implicit and explicit FEM software

A dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current "Multicore+GPU" systems.

MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming.

The Intel Math Kernel Library

MOLGW is a Gaussian-type orbital code for finite systems. It implements a self-consistent mean-field calculation, followed by a many-body perturbtation theory post-treatment.

Semi-empirical software package.

MPI for Python

MUMPS: a MUltifrontal Massively Parallel sparse direct Solver

Numerical Algorithms Group (NAG) libraries

A multidisciplinary structural analysis application used by engineers to perform static, dynamic, and thermal analysis.

 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs.

NCL is a free interpreted language designed specifically for scientific data processing and visualization.

Ncview is a X Windows visual browser for netCDF data format files.

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Fortran interface of NetCDF, a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.

Ninja is a small build system with a focus on speed.

NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data.

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

Open Field Operation and Manipulation: CFD Toolbox 

OpenMolcas is a quantum chemistry software package developed by scientists

Ab initio quantum chemistry program package

An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.

PERTURBO is an open source software to compute from first principles the scattering processes between charge carriers (electrons and holes) and phonons, defects, and photons in solid state materials, including metals, semiconductors, oxides, and insulators.

Exploration and testing of linear solvers, matrix operations

Utilities for manipulating SAM files

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.

A high-performance parallel I/O library for accessing Unidata's NetCDF

Protocol Buffers - Google's data interchange format

py-spy is a sampling profiler for Python programs

Python programming language

Ab initio quantum chemistry package

Qiskit is an open-source SDK for working with quantum computers at the level of circuits, algorithms, and application modules.

Cross-platform application and GUI framework

QuTiP is open-source software for simulating the dynamics of open quantum systems.

Ray provides a simple, universal API for building distributed applications.

A modular scientific software framework

Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Profiler for parallel scientific and engineering applications

SciPy (pronounced “Sigh Pie”) is open-source software for mathematics, science, and engineering.

The Score-P is a highly scalable tool suite for profiling, event tracing, and online analysis of HPC applications.

A tool for processing sequences in FASTA or FASTQ format.

Electronic structure calculations and ab-initio molecular dynamics of molecules and solid

The Software for Linear Algebra Targeting Exascale (SLATE) provides fundamental dense linear algebra capabilities to the high-performance computing (HPC) community.

SnpEff is a toolthat annotates and predicts the effects of variants on genes (such as amino acid changes).

Accelerating High-performance application parallelization.

Software pipeline for building loci from short-read sequences

STAR-CCM+ delivers the entire engineering simulation process in a single integrated software environment.

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

Szip is an implementation of the extended-Rice lossless compression algorithm. 

TecIO is the library supplied with Tecplot 360 that enables third-party applications to output solution data directly to Tecplot binary-formatted files.

TensorFlow is an open-source library of software for dataflow and differential programing for various tasks.

Faster fault isolation, improved memory optimization, and dynamic visualization for your high-scale HPC apps

A flexible read trimming tool for Illumina NGS data

Valgrind is an instrumentation framework for building dynamic analysis tools

Vienna Ab initio Simulation Package: atomic scale materials modelling

Variant Effect Predictor

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Wannier90 is an open-source code (released under GPLv2) for generating maximally-localized Wannier functions and using them to compute advanced electronic properties of materials with high efficiency and accuracy.

IBM Watson Machin Learning and Deep Learning Framework

WxWidgets is a free and open source cross-platform C++ framework for writing advanced GUI applications using&nbsp

A suite of light-weight libraries to work with XML in Fortran.

Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.