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Science Software

Mathematics:

  • OpenStat - OS4 was originally written as an aid to students and teachers for introductory and advanced statistics courses, primarily in the social sciences.
  • Octave [GNU GPL] - GNU Octave is a high-level language, primarily intended for numerical computations.
  • Scilab - Open source platform for numerical computation
  • Maxima [GNU GPL] - Maxima is a system for the manipulation of symbolic and numerical expressions, including differentiation, integration, Taylor series, Laplace transforms, ordinary differential equations, systems of linear equations, polynomials, and sets, lists, vectors, matrices, and tensors.
  • wxMaxima [GNU GPL] - wxMaxima is a cross platform GUI for the computer algebra system maxima based on wxWidgets.
  • SciCraft [GNU GPL] - SciCraft is a powerful open source data analysis software with an easy-to-use graphical user interface.
  • Yacas [GNU GPL] - YACAS is an easy to use, general purpose Computer Algebra System, a program for symbolic manipulation of mathematical expressions.
  • The R Project - R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.
  • R Commander [GNU GPL] - The R-Commander GUI consists of a window containing several menus, buttons, and information fields.
  • SciViews-R [GNU GPL] - SciViews-R is a suite of companion applications that provides a Graphical User Interface (GUI) on top of the command-line driven environment of R.
  • JGR (Java Gui for R) [GNU GPL] - JGR (speak 'Jaguar') is a universal and unified Graphical User Interface for R.
  • SciPy [BSD license] - SciPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering.
  • Rlab - Rlab is an interactive, interpreted scientific programming environment. Rlab is a very high level language intended to provide fast prototyping and program development, as well as easy data-visualization, and processing.
  • GAP [GNU GPL] - GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.
  • MayaVi [BSD] - MayaVi is a free, easy to use scientific data visualizer.
  • PARI/GP [GNU GPL] - PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...).
  • Numerical Python - Numerical Python adds a fast and sophisticated array facility to the Python language.
  • SalStat [GNU GPL] - Rapid statistical analysis of scientific data under the GPL.
  • MacAnova [GNU GPL] - MacAnova is a free, open source, interactive statistical analysis program for Windows, Macintosh, and Linux.
  • Elmer [GNU GPL] - Elmer is an open source multiphysical simulation software developed by CSC.


Biology:

  • GROMACS [GNU GPL] - GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
  • GENtle [GNU GPL] - GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more.
  • ClustalX - Multiple sequence alignment program.
  • GeneDoc - A Full Featured Multiple Sequence Alignment Editor, Analyser and Shading Utility for Windows.
  • E-Cell - E-Cell is a concept of constructing virtual cells on computers.
  • Open Bioinformatics Foundation - The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics.
  • BioPython - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
  • BioPerl - BioPerl project's community documentation site.
  • BioJava - BioJava is an open-source project dedicated to providing a Java framework for processing biological data.
  • BioRuby - BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language.
  • BioSQL/OBDA - OBDA is standard developed by the Open Bioinformatics Foundation to standardize the way projects access sequence data resources.
  • BioMOBY - The MOBY system for interoperability between biological data hosts and analytical services.
  • BioDAS - Open Source system for exchanging annotations on genomic sequence data.
  • Artemis [GNU GPL] - Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
  • PyMOL - PyMOL is a USER-SPONSORED molecular visualization system on an OPEN-SOURCE foundation.
  • OpenRasMol - Molecular Graphics Visualisation Tool.
  • Bioconductor [BSD or GPL] - Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data.
  • Staden [BSD] - A fully developed set of DNA sequence assembly (Gap4), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Geographic Information Systems:

  • QGIS [GNU GPL] - Quantum GIS (QGIS) is a user friendly Open Source Geographic Information System (GIS) that runs on Linux, Unix, Mac OSX, and Windows.
  • GRASS GIS [GNU GPL] - Geographic Resources Analysis Support System.
  • MapServer [Mapserver License] - MapServer is an Open Source development environment for building spatially-enabled internet applications.
  • GDAL [X/MIT style] - is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation.
  • OpenEV [X/MIT style] - OpenEV is a software library and application for viewing and analysing raster and vector geospatial data.
  • Thuban [GNU GPL] - Thuban is an Interactive Geographic Data Viewer.
  • JUMP [GNU GPL] - The Unified Mapping Platform (JUMP) is a GUI-based application for viewing and processing spatial data. It includes many common spatial and GIS functions.
  • Virtual Terrain Project [VTP Software Licence] - The goal of VTP is to foster the creation of tools for easily constructing any part of the real world in interactive, 3D digital form.

General:

  • Celestia [GNU GPL] - The free space simulation that lets you explore our universe in three dimensions. Celestia runs on Windows, Linux, and Mac OS X.
  • OpenUniverse [GNU GPL] - it's a piece of software, simulating the Solar System's bodies in 3D on your Windows or Linux PC.
  • Stellarium [GNU GPL] - Stellarium is a free open source planetarium for your computer. It shows a realistic sky in 3D, just like what you see with the naked eye, binoculars or a telescope.
  • Virtual Moon [GNU GPL] - Free software for Moon observation or survey.
  • GNUPlot - Gnuplot is a portable command-line driven interactive data and function plotting utility for UNIX, IBM OS/2, MS Windows, DOS, Macintosh, VMS, Atari and many other platforms.
  • Walnut [GNU GPL/LGPL] - Walnut is an OpenSource framework for the development of neural network simulations by both beginners and experts. It is a system that is extensible with new paradigms. Neural network architectures and simulations are portable between various platforms (notably Windows and Unix).
  • CopperCore [GNU GPL] - CopperCore, a J2EE runtime engine for IMS Learning Design which can be used to incorporate IMS Learning Design in your own application(s).
  • Gwyddion [GNU GPL] - Gwyddion is a modular program for SPM (scanning probe microscopy) data visualization and analysis.


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