3DSlicer 3D Slicer (Slicer) is a free, open source software package for image analysis and scientific visualization.
AMPHORA AMPHORA ("AutoMated Phylogenomic infeRence Application") is an open-source bioinformatics workflow.
Analysis of Functional NeuroImages Analysis of Functional NeuroImages (ADJ) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity.
AnimatLab (software) AnimatLab is an open-source neuromechanical simulation tool that allows authors to easily build and test biomechanical models and the neural networks that control them to produce behaviors.
ANUGA Hydro ANUGA Hydro is a free and open source software tool for hydrodynamic modelling, suitable for predicting the consequences of hydrological disasters such as riverine flooding, storm surges and tsu...
Archaeological Recording Kit Archaeological Recording Kit (ARK) is a collection of web-based tools for collection, storage and dissemination of archaeological data.
Ascalaph Designer Ascalaph Designer is a general purpose molecular modelling package for molecular design and simulations.
Astronomy Calculators (software) Astronomy Calculators is a collection of software utilities designed to perform optical and telescopic calculations and conversions, and also provide astronomical data in the form of ephemerides...
Astropy The Astropy Project is a collection of software packages written in the Python programming language and designed for use in astronomy.
Avogadro (software) Avogadro (software) is a molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Bioconductor Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
BioModels Database BioModels Database is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest.
Biopython The Biopython Project is an international association of developers of non-commercial Python tools for computational molecular biology, as well as bioinformatics.
Biskit Biskit is an open source software package written in Python.
Blue Obelisk Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005.
Brian (software) Brian is an open source Python package for developing simulations of networks of spiking neurons.
BRP-PACU BRP-PACU is a dual channel FFT audio analysis tool.
Calypso Ichthyological Database The Calypso Ichthyological Database numbering system is an open source free repository allowing the unique identification numbering of all fish species with a six-numeral fixed number.
CellProfiler CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automat...
Chemistry Development Kit The Chemistry Development Kit is an open-source Java library for Chemoinformatics and Bioinformatics.
Chemtool Chemtool is a free software program for drawing chemical structural formulas, written in C using GTK for Unix and Linux.
Citcom CitCom (for California Institute of Technology Convection in the Mantle) is a finite element code designed to solve thermal convection problems relevant to earth's mantle released under th...
Clone manager Clone Manager is a commercial bioinformatics software work suite of Sci-Ed, that supports molecular biologists with data management and allows to perform certain in silico preanalyis.
Cn3D Cn3D is a Windows, Macintosh and Unix-based software from the United States National Library of Medicine that acts as a helper application for web browsers to view three-dimensional structures f...
Code Saturne Code_Saturne is a general purpose computational fluid dynamics free computer software package.
Coot (program) The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer gr...
DataScene DataScene is a scientific graphing, animation, data analysis, and real-time data monitoring software package.
DAVID (bioinformatics tool) DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenes...
EMBOSS EMBOSS is an acronym for European Molecular Biology Open Software Suite.
Emergent (software) Emergent (formerly PDP++) is neural simulation software that is primarily intended for creating complex, sophisticated models of the brain and cognitive processes, but can also be used for any t...
Encog Encog is a machine learning framework available for Java, .Net, and C++.
EXCITING Exciting is a state-of-the-art full-potential linearized augmented plane wave (FP-LAPW) code which uses quantum mechanics, specifically density functional theory (DFT), to determine the physical...
EXMARaLDA EXMARaLDA is a set of free software tools for creating, managing and analyzing spoken language corpora.
Experix Experix is an open-source command interpreter designed for operating laboratory equipment, especially data acquisition devices, and processing, displaying and storing the data from them.
Feature Selection Toolbox Feature Selection Toolbox (FST) is a machine learning software focusing primarily on the feature selection problem, written in C++, developed at the Institute of Information Theory and Automatio...
Fityk Fityk is a curve fitting and data analysis application, predominantly used to fit analytical, bell-shaped functions to experimental data.
Foldit Foldit is an online puzzle video game about protein folding.
FreeFem++ FreeFem++ is a programming language and a software focused in solving partial differential equations using the finite element method.
FuncDesigner FuncDesigner is a free computer algebra system written as a Python module.
Geant4 Geant4 (for GEometry ANd Tracking) is a platform for "the simulation of the passage of particles through matter," using Monte Carlo methods.
Gene Designer Gene Designer is a free bioinformatics software package.
General Architecture for Text Engineering General Architecture for Text Engineering or GATE is a Java suite of tools originally developed at the University of Sheffield beginning in 1995 and now used worldwide by a wide community ...
GenMAPP GenMAPP (Gene Map Annotator and Pathway Profiler) is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways (metabolic, signal...
Gensim Gensim is an open-source vector space modeling and topic modeling toolkit, implemented in the Python programming language, using fast C and Fortran system libraries for performance.
Marble (software) Marble is a virtual globe that allows the user to choose among the Earth, the Moon, Venus, Mars and other planets.
MDynaMix MDynaMix (an acronym for Molecular Dynamics of Mixtures) is a general purpose molecular dynamics software package for simulations mixtures of molecules, interacting by AMBER/CHARMM like for...
MicroDicom MicroDicom is a free DICOM viewer for Windows.
Mimee Mimee is a program which can convert geographical coordinates between various datums and formats.
MLPACK (C++ library) MLPACK is a machine learning software library for C++, built on top of the Armadillo library.
MOEA Framework The MOEA Framework is an open-source evolutionary computation library for Java that specializes in multi-objective optimization.
MoFEM JosePH MoFEM (Mesh Orientated Finite Element Method) is an open source finite element analysis code developed and maintained at the University of Glasgow.
Molekel Molekel is a free software multiplatform molecular visualization program.
Montage Image Mosaic Software Montage is a software toolkit used in astrophotography to assemble astronomical images in Flexible Image Transport System format into composite images, called mosaics, that preserve the calibrat...
NAMD NAMD (Not (just) Another Molecular Dynamics program) is a freeware molecular dynamics simulation package written using the Charm++ parallel programming model, noted for i...
NEST (software) NEST is a simulation software for spiking neural network models, including large-scale neuronal networks.
NoeClone NoeClone is a bioinformatics software which can run in multiple operating systems with the same interface.
NumPy NumPy is an extension to the Python programming language, adding support for large, multi-dimensional arrays and matrices, along with a large library of high-level mathematical functions to oper...
NWChem NWChem is an ab initio computational chemistry software package which also includes quantum chemical and molecular dynamics functionality.
octopus (software) octopus is a software package for performing Kohn–Sham density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations.
OELib OELib was an Open Source Cheminformatics library.
Olex2 Olex and Olex2 are versatile software for crystallographic research.
Open Babel OpenBabel is free software, a chemical expert system mainly used for converting chemical file formats.
Open Source Physics Open Source Physics, or OSP, is a project sponsored by the National Science Foundation and Davidson College, whose mission is to spread the use of open source code libraries that take care of a ...
OpenBabel OpenBabel is free software, a chemical expert system mainly used for converting chemical file formats.
OpenFOAM OpenFOAM (Open source Field Operation And Manipulation) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mec...
OpenMS OpenMS is an open-source project for data analysis and processing in protein mass spectrometry and is released under the 3-clause BSD licence.
OpenOpt OpenOpt is a framework for numerical optimization, nonlinear equations and systems of them.
Orbit-Vis Orbit-Vis is an orbit simulation program which is designed to allow users to simulate a satellite in any orbit around the Earth, and to give the user data on the position and motion of the satel...
OsiriX OsiriX is an image processing application for Mac dedicated to DICOM images (".dcm" / ".DCM" extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...).
PathVisio PathVisio is a free open-source pathway analysis and drawing software.
Perl Data Language Perl Data Language (abbreviated PDL) is a set of free software array programming extensions to the Perl programming language.
Phyloscan Phyloscan is a web service for DNA sequence analysis that is free and open to all users (without login requirement).
Physics Analysis Workstation The Physics Analysis Workstation (PAW) is an interactive, scriptable computer software tool for data analysis and graphical presentation in High Energy Physics (HEP).
ProteoWizard ProteoWizard is a set of open-source, cross-platform tools and libraries for proteomics data analyses.
Ptolemy Project (computing) The Ptolemy Project is an ongoing project aimed at modeling, simulating, and designing concurrent, real-time, embedded systems.
Pwpaw PWPAW A Projector Augmented Wave (PAW) code for electronic structure calculation.
PWscf PWscf (Plane-Wave Self-Consistent Field) is a set of programs for electronic structure calculations within density functional theory and density functional perturbation theory, using plane...
PyEphem PyEphem is a library that implements astronomical algorithms for the Python programming language.
PyMOL PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated...
Python SCOOP (software) SCOOP (Scalable Concurrent Operations in Python) is a Python software module for distributing concurrent tasks on various environments, from heterogeneous grids of workstations to supercom...
QuteMol QuteMol is an open source, interactive, molecular visualization system.
RasMol RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecule structures, such as those foun...
Registax RegiStax is image processing software for amateur astrophotographers, released as freeware, which runs under Windows.
Rmetrics Rmetrics is a free, open source and open development software project for teaching Computational Finance.
ROOT ROOT is an object-oriented program and library developed by CERN. It was originally designed for particle physics data analysis and contains several features specific to this field, but it is al...
RQDA RQDA is an R package for computer assisted qualitative data analysis or CAQDAS. It is installable from, and runs within, the R system, but has a separate window running a graphical user interfac...
Rule-based modeling Rule-based modeling is a modeling approach that uses a set of rules that implies a model.
SCaViS SCaViS is an interactive framework for scientific computation, data analysis and data visualization designed for scientists, engineers and students.
ScientificPython ScientificPython is an open source library of scientific tools for the Python programming language.
SciPy SciPy is a computing environment and open source ecosystem of software for the Python programming language used by scientists, analysts and engineers doing scientific computing and technical co...
Seismic Unix Seismic Unix is an open source seismic utilities package supported by the Center for Wave Phenomena (CWP) at the Colorado School of Mines (CSM).
ShelXle The program ShelXle is a graphical user interface for the structure refinement program SHELXL. ShelXle combines an editor with syntax highlighting for the SHELXL-associated .ins (input) and .re...
SimPy SimPy is a free process-based, object-oriented discrete-event simulation language in Python.
Spyder (software) Spyder (formerly Pydee) is an open source cross-platform IDE for scientific programming in the Python language.
Stanford University Unstructured SU2 (Stanford University Unstructured) is a suite of open-source software tools written in C++ for the numerical solution of partial differential equations and performing PDE constrained o...
Systems Biology Ontology The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling.
Tanagra (machine learning) Tanagra is a free suite of machine learning software for research and academic purposes developed by Ricco Rakotomalala at the Lumière University Lyon 2, France.
The OpenMS Proteomics Pipeline The OpenMS Proteomics Pipeline (TOPP) is a set of computational tools that can be chained together to tailor problem-specific analysis pipelines for HPLC-MS data.
TINKER TINKER is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for bio...
Tinker (software) Tinker is a computer software application for molecular dynamics simulation with a complete and general package for molecular mechanics and molecular dynamics, with some special features for bio...
Trans-Proteomic Pipeline The Trans-Proteomic Pipeline (TPP) is a widely used freely available open-source proteomics data analysis pipeline developed at the Institute for Systems Biology (ISB) by the Ruedi Aebersold gro...
UGENE UGENE is free open-source cross-platform bioinformatics software.
Uniform Sequence Address In the Bioinformatics EMBOSS software package, a Uniform Sequence Address (USA) is a string defining how the software accesses a biological sequence.
Vector NTI Vector NTI is a bioinformatics software package.
ViewMol3D ViewMol3D is a 3D OpenGL viewer for molecular structures from the output of quantum chemistry calculations.
Visualization Library Visualization Library is an open source C++ middleware for 2D/3D graphics applications based on OpenGL 2.1, designed to develop portable applications for the Microsoft Windows, Linux/X11 and Mac...
Vortexje Vortexje is open-source computational fluid dynamics (CFD) software created by Baayen & Heinz GmbH in 2011.
VTK The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization.
Waffles (machine learning) Waffles is a collection of command-line tools for performing machine learning operations developed at Brigham Young University.
Weka (machine learning) Weka (Waikato Environment for Knowledge Analysis) is a popular suite of machine learning software written in Java, developed at the University of Waikato, New Zealand.
XDrawChem XDrawChem is a free software program for drawing chemical structural formulas, available for Unix and Mac OS. It is distributed under the GNU GPL. In Microsoft Windows this program is called Win...
XMD XMD is a classical molecular dynamics software designed to simulate problems related to materials science.