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.

Amsterdam Modelling Suite- computational chemistry software for cheistry and materials science research.

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

Bazaar is a version control system that helps you track project history over time and to collaborate easily with others

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.

Basic Linear Algebra Subprograms

Blat is an alignmet tool for proteic and genomic sequences

Bowtie is an ultrafast, memory-efficient short read aligner.

Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.

This fork of BVLC/Caffe is dedicated to improving performance of this deep learning framework when running on CPU, in particular Intel® Xeon processors (HSW+) and Intel  Xeon Phi processors. This module contains Intel/Caffe with MLSL support for multi-node training/inference.

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.

 COMSOL Multiphysics® è una piattaforma di simulazione che offre capacità di modellazione multifisica e monofisica completamente accoppiate.

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

Cricetulus griseus (Chinese hamster) - RefSeq assembly 1.0

Solid state chemistry and physics

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.

Tools for exploring deep sequencing data

The DIRAC program computes molecular properties using relativistic quantum chemical methods. 

General purpose classical molecular dynamics (MD) simulation software 

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

An extensible, customizable, free/libre text editor — and more.

Instrumentation framework to generate execution traces of the most used parallel runtimes

validate and manipulate fastq files

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 versatile software 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.

GNU Compiler Collection

Grace is a WYSIWYG 2D plotting tool

GROningen Machine for Chemical Simulations - Molecular Dynamics on Parallel Computers

GNU Triangulated Surface Library

HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.

Graph-based alignment of next generation sequencing reads to a population of genomes

Altair Hyperworks is the most comprehensive, open architecture CAE simulation platform in the industry, offering the best technologies to design and optimize high performance, weight efficient and innovative products.

This module comprehend genomic data from Bos taurus (cow). Sequences,

Indexes and Annotations of the genome are present.

 Ready-To-Use Reference Sequences and Annotations provided by illumina

Ready-To-Use Reference Sequences and Annotations

Intel compilers

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

Java Runtime Enviroment

The Juelich benchmarking environment (JUBE) provides a script based

framework to easily create benchmark sets, run those sets on different

computer systems and evaluate the results.

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.

Libidn2 is an implementation of the IDNA2008 + TR46 specifications (RFC 5890, RFC 5891, RFC 5892, RFC 5893, TR 46)

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

Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq)

GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text.

METIS is a software package for graph partitioning that implements various multilevel algorithms

Quantum Chemistry Program

Quantum Chemistry Package. Ab-initio molecular electronic stucture with full electron-correlation

A C library for multiple-precision floating-point computations

Movie player.

BSD-licensed implementation of the MPI standard

Scalable molecular dynamics for biomolecular modeling

A discovery tool for chemical insights from complex wavefunctions. 

A set of FREE application programs implementing the File Transfer Protocol (FTP)

NetCDF Operators

NEST is a simulator for spiking neural network models focusing on the dynamics, size and structure of neural systems.

C++ 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.

NEURON simulation environment

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 

The free and opensource java implementation

OpenMolcas is a quantum chemistry software package developed by scientists

Ab initio quantum chemistry program package

A program for the ab initio investigation of crystalline solids

Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations

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

Open-source collection of electronic structure modules powered by Python.

PyTorch is an open source machine learning library

QE is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale based on density-functional theory, plane waves, and pseudopotentials.

Quantum-suite is a module that contains the most important sdk for quantum computing available today.

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

Containarization tool for HPC

SLEPc is a software library for the solution of large sparse eigenproblems on parallel computers.

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

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archive and download them locally

Spliced Transcripts Alignment to a Reference

Stata is a complete, integrated software package that provides data manipulation, visualization, statistics, and automated reporting.

SU2 is an open-source collection of software tools written in C++ and Python for the analysis of partial differential equations (PDEs) and PDE-constrained optimization problems on unstructured meshes with state-of-the-art numerical methods.

Generic indexer for TAB-delimited genome position files.

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

A spliced read mapper for RNA-Seq

The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems.

USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.

VCFtools is a program package designed for working with VCF files.

VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool

Intel VTune Amplifier performance analysis toolkit

WannierTools is a software for investigation of novel topological materials.

Xiamen Valence Bond (XMVB) is a valence bond (VB) theory based quantum chemistry program for performing electronic structure calculations

LibYAML is a YAML parser and emitter library