Free Software :: Scientific Software

Scientific Publication Portals

• PLoS ("Public Library of Science". Online library of free scientific publications. License: Creative Commons Attribution License.)
• Bio Informatics (An international organization, of about 3000 members, which promotes freedom and openness in the field of bioinformatics.) (projects) (cvs) (ml)
• BioMed / Chemistry / PhysMath central (Open access science repository)
• PubChem (Information portal on the biological activities of small molecules. License: none, it is public domain)

'Free-for-non-commercial-use' Scientific Publication Portals

• SciDev ("Science and development network")
• Journal of Vision (Periodical about the visual functions in organisms.)

Scientific Software Portals (non-specific)

• SourceForge Scientific/Engineering Projects
• FreshMeat Scientific/Engineering Projects
• AI Foundry (Portal for free software projects related to the field of Artificial Intelligence (ml)
• FermiTools (FermiLab's public software. License: BSD-style)

Data Management Tools

• Databases (Database engines, development and management tools)
• HDF5 (C++ library and storage format for handling scientific data. License: BSD-style)
• h5utils (Collection of utilities for visualization and conversion of scientific data in the standard HDF5 format. License: BSD-style and GPL)
• netCDF ("Network Common Data Form". Interface definition and tools for array-oriented data access. License: BSD-style)
• Comedi (Linux kernel object for access to common data acquisition plug-in boards and an user-land library) (cvs) (ml)
• libRASCH (Pluggable C library which provides a common interface for viewing and processing of measurement data which is stored in different data formats) (ml)
• OGDL ("Ordered Graph Data Language". Structured textual format parser, implemented in C and Perl, for representing graphs. License: BSD-style) (cvs) (ml)

Plotting & Graphing Tools

• GnuPlot (Interactive 2D/3D plotting tool) (cvs) (ml) (deb)
• Graphviz (Collection of tools for visualizing graphs. License: Common Public License) (ml)
• R (Scheme-alike language and run-time environment for statistical computing and 2D/3D graphics) (ml)
• GD (C based library for the dynamic creation of PNG/JPEG images. License: BSD-style) (Perl GD Perl interface for GD) (Artichow PHP interface for GD) (forum)
• QtiPlot (Qt based tool for the creation of 2D/3D plots and graphs)
• Matplotlib (Python based library for the creation of 2D plots and graphs. License: Python Software Foundation) (cvs) (ml)
• Veusz (Python/Qt based plotting 2D plotting tool.) (cvs) (ml)
• Asymptote (C++-like vector-graphics scripting language for 2D technical drawings. Asymptote is inspired by MetaPost.) (cvs) (ml) (forum)
• LabPlot (KDE based 2D/3D plot tool)
• Ploticus (Flexible command-line tool to create 2D plots and graphs) (forum)
• Cug (GTK+ based 2D/3D plot tool)
• RLPlot (Qt based interactive 2D plotting tool) (cvs)
• Guppi (GNOME based 2D/3D plot tool) (ml)
• Fityk (wxWidgets based nonlinear curve fitting and data analysis tool)
• QoscC (Qt based software Oscilloscope)
• SciGraphica (GTK+ based 2D/3D plot tool. Inactive project.) (cvs) (ml)
• Pigale (2D/3D graph editing tool and a C++ based algorithm library for planar graphs.) (cvs)
• Grace (X-Window/Mot*f based tool to create 2D plots and graphs) (ml) (GraceTMPL C++ library to save data as Grace files, optionally using a template file) (cvs)
• Springgraph (Perl script for the visualization of 2D/3D graphs. Springgraph can read the .dot file format.) (deb)
• Tulip (Tool for the visualization of large 2D/3D graphs)
• NetworkX (Python based network graphs tool) ( ml)
• TreeView X (Tool for viewing phylogenetic trees in NEXUS/Newick file format)
• KMatplot (KDE based 2D/3D plot tool. Inactive project.) (cvs) (ml)
• PyX (Python based tool for the creation of 2D/3D encapsulated PostScript figures) (cvs) (ml)
• linSmith (GTK+ based Smith chart tool) (forum)
• Surf (Algebraic geometry visualization tool) (cvs) (ml)
• Eukleides (Euclidean geometry drawing language, compiler and interactive GUI tool)
• Graph (GTK+/GTKmm based application to create and manipulate graphs.)
• PLplot (Library of functions that are useful for making scientific plots. PLplot functions can be called from C, C++, FORTRAN, Python and Tcl.) (cvs) (ml)
• xd3d (Xlibs/Fortran77 based 2D/3D plot tool)
• geg (GTK+ based equation grapher. Inactive project.)
• g3data (GTK+ based tool for extracting data from graph images)
• GtkDataBox (GTK+ based GUI widget to dynamically display large amounts of numerical data)
• Tacal (GNOME based mathmatics tool to compute real, complex, matrix and curve series)
• Fityk (wxWidgets based tool for nonlinear curve-fitting and data analysis) (cvs) (ml)
• SalStat (wxPython based statistical data management/analysis/graphics tool)
• DAP (Statistical data management/analysis/graphics tool)
• Statist (Console based statistics tool)

Numerical and Algorithmic Tools

- Numerical and Algorithmic Libraries

• C based Numerical, Algorithmic and Crypto Libraries (from the C section)
• C++ based Numerical, Algorithmic and Crypto Libraries (from the C++ section)

- Spreadsheet Tools

• Gnumeric (GNOME based spreadsheet application) (ml)
• KSpread (KDE based spreadsheet application) (ml)
• OpenOffice Spreadsheet (cvs) (ml)

- Desktop Calculators

• Qalculate! (GTK+ based scientific calculator) (cvs) (ml)
• galculator (GTK+ based scientific calculator) (cvs) (ml)
• SpeedCrunch (Qt based high precision calculator)
• GraphCalc (KDE based scientific calculator with support for 2D/3D graphing) (cvs) (ml)
• RPC (Ncurses based RPN calculator)

- Numerical and Algorithmic Frameworks

• Gnu Octave (High-level interactive language for numerical computations) (cvs) (ml)
• Sage (Python based Mathmatics research platform)
• Quantian (Debian GNU/Linux Knoppix variant tailored to numerical and quantitative analysis tasks)
• PDL (Perl based numerical toolkit, with support for 2D/3D visualization) (cvs) (ml)
• Scipy (Python based numerical tooikit, with support for 2D/3D visualization) (cvs) (ml)
• Singular (Computer algebra system, for polynomial computations with special emphasis on the needs of commutative algebra, algebraic geometry, and singularity theory. Users program in a C-like programming language.) (forum)
• PARI/GP (Computer algebra system, designed for fast computations in number theory.) (cvs) (ml)
• Ginac (C++ based mathematical engine for symbolic computations) (cvs) (ml)
• Kalamaris (Mathematical engine for symbolic computations with a distributed design and a KDE/OpenGL based client)
• gTybalt (C++ based mathematical engine for symbolic computations, build upon: Ginac, Cint and GSL)
• Maxima (LISP based mathematical engine for symbolic computations) (cvs (forum)
• Mathomatic (C based mathematical engine for symbolic computations)
• LinPacker (Qt based tool to find optimal packings within a rectangular plain)
• LBT (LTL to Buüchi automata conversion tool)
• KMonodim (KDE based tool for solving monodimensional particle-in-a-box problems)
• PETSc (Suite of data structures and functions for MPI-based parallel programming solutions for scientific applications using partial differential equations)
• IBEN (Interactive BDD Environment. Command-line tool for teaching 'reduced ordered binary decision diagrams' using the BuDDy C++ library.) (cvs)
• MuDDy (SML language interface to the BuDDy C++ library for doing binary decision diagramming)
• py_ecc (Python functions for Reed-Solomon codes, finite field arithmetic, and generic matrix operations)

Technical Process Analysis & Simulation

• Gambit (C++ library for simulating/analysing game theory. Gambit includes a wxWidgets based user tool.) (cvs) (ml)
• PVbrowser ("Process View Browser". Qt based tool for the visualization of industrial/technical processes) (cvs)
• KSimus (KDE based tool for the simulation, automatization and visualization of technical processes) (cvs) (ml)
• Dakota (3D geometric design analysis kit for structure/optimization analysis and terascale applications)
• TCM ("Toolkit Conceptual Modeling". X based tools for representing conceptual models of software systems. Inactive project.)

Natural Process Analysis & Simulation (not chemistry/biology/astronomy specific)

• VTK (Visualization ToolKit. 3D geometric design analysis kit for structure/optimization analysis and terascale applications. License: BSD-style) (ml)
• GFS ("Gerris Flow Solver". C library for solving partial differential equations describing fluid flow.) (cvs) (ml)
• CAMFR ("CAvity Modelling FRamework". C++/Pyhton based simulation tool for the propagation of electromagnetic waves, using a frequency-domain approach, according to Maxwell's equations)
• Radar FDTD (3D FDTD simulation tool which can compute the propagation of electromagnetic waves according to Maxwell's equations)
• SnowPath (Models the process of people forming paths in the snow as they walk across open spaces)
• Vis5D (Fortran/GTK+/OpenGL based volumetric visualization program for scientific "HDF5" datasets in 3+ dimensions. Vis5D is being used as a weather forecast system. Inactive project.) (cvs) (ml)
• OpenQVis (Framework for the visualization of 3D volume data on a uniform rectilinear grid, as they arise from tomographic measurement or numerical simulation. Inactive project.) (cvs) (ml)
• Hasas ("Hydro Acoustic Signal Analysis System". GTK+ based tool for passive sonar signal analysis. Hasas has support for: ALSA, FLAC and Comedi. Inactive project.) (cvs)
• Dakota (3D geometric design analysis kit for structure/optimization analysis and terascale applications. Inactive project.)
• CanDetect (Tool to identify hidden corrosion on aircrafts via an Eddy current probe. Inactive project. License: BSD-style) (cvs)

Chemistry

• PyMol (C/Python/Tcl-Tk based 3D molecular modeling system. License: Python License) (cvs) (ml)
• Ghemical (GNOME based molecular modeling tool. Inactive project.)
• polyXmass (Mass spectrometry data analysis tool for a variety of polymers)
• Viewmol (Python/Motif based tool to graphically aid in the generation of 3D molecular structures for computations and to visualize their results.)
• OpenBabel (Toolkit to convert between many file formats used in molecular modeling and computational chemistry) (cvs) (ml)
• XDrawChem (Qt based molecule structure drawing tool)
• EasyChem (GTK+ based molecule structure drawing tool)
• BKchem (Python/Tk based molecule structure drawing tool) (cvs) (ml)
• OpenRasMol (Tcl/Tk based molecule structure drawing tool)
• Moscito (Toolkit for condensed phase and gas phase molecular dynamics simulation)
• CRK ("Chemical Resource Kit". Collection of chemistry software for tasks like: data archival, data entry and presentation of chemical information)
• EMAN (Qt based scientific image processing suite used for reconstructing 3D models from a set of randomly oriented particle images)
• ABINIT (Toolset to find the total energy, charge density and electronic structure of systems made of electrons and nuclei within Density Functional Theory, using pseudo potentials and a "planewave basis".)
• Nano-Hive (Simulator used for modeling the physical world at a nanometer scale. Currently w32-only.) (ml)
• GPeriodic (GNOME based periodic table viewer. Inactive project.)

Biology

• WikiSpecies (Collaboratively build, species directory project. WikiSpecies is related to the Wikipedia encyclopedia project. License: GNU FDL)
• PLoS Biology ("Public Library of Science". Online library of free scientific publications. License: Creative Commons Attribution License.)
• Bio Informatics (An international organization, of about 3000 members, which promotes freedom and openness in the field of bioinformatics.) (projects) (cvs) (ml)
• BioPerl (Perl based software portal for processing biological data) (cvs) (ml)
• BioPython (Python based software portal for processing biological data) (cvs) (ml)
• BioForge (Software development portal for bio-technology related software. BioForge is part of the BIOS project. License: The CAMBIA BIOS License)
• E-Cell (Python/GSL/GNOME based simulation environment for researching biological cell theories) (cvs)
• BTK (Biomolecule Tookit. C++ based library for modeling biological macro-molecules such as proteins, DNA and RNA.) (cvs)
• Ensembl (Initiative to create a software system which produces and maintains automatic annotation on eukaryotic genomes) (cvs) (ml)
• BLAST2 (Nucleotide/protein sequence alignment program. License: none, it is public domain)
• Biodas (Project to create a system for exchanging annotations on genome sequence data) (cvs) (ml)
• MuGeN (GTK+ based tool for visualizing annotated genome sections)
• DNA Linux (SLAX GNU/Linux based live-CD variant tailored to bio-information related tasks) (ml)

Astronomy

• "Linux Astronomy HowTo"
• Nova (GNOME based 'integrated observational environment' which combines image capturing, telescope control and ephemeris functionality) (cvs) (ml)
• LfA ("Linux for Astronomy". Portal for astronomical software and documentation usable on GNU/linux)
• StarPlot (GTK+ based 3D galaxy/star map viewer)
• SpaceChart (GNOME based 3D galaxy/star map viewer)
• ORSA ("Orbit Reconstruction, Simulation, and Analysis". C++ based framework for the development of algorithms for the simulation and analysis of the orbital evolution of bodies in space) (cvs) (ml)
• Skyviewer (Qt based 3D galaxy/star map viewer)
• Solar System (Command-line application to simulate the orbits of the Sun and the nine main planets in our Solar System. The results can be plotted with GnuPlot.)

Geospatial Science

- Free Geospatial Data

• OpenStreetMap (Initiative to create free street maps) (ml)
• Open Source Geospatial Foundation (Effort to support and build the high-quality, free geospatial software) (ml)
• GIS Data Depot (Collection of public-domain geo-data covering places all over the world)
• TopoWest (Collection of scanned topographical maps covering places in the USA. License: FreeTopo copyleft license)
• USA National Atlas (Public-domain geo-data about the USA. Available formats: SDTS, E00, Shape and TIFF.)
• OpenGuides (Initiative to create free city guides) (ml)
• GeoIP (IP-location database and a set of libraries for accessing the database. License: GPL for the libraries and OpenData License for the database)
• GeoURL (URL-location database and a set of libraries for accessing the database. License: ?
• geograph.org.uk (Geographic material for the British Isles. License: ...)

- GPS Tools

• NavIT (Navigation system with routing engine)
• GPX (XML based data format specification for exchanging GPS data between applications. License: public domain) (forum)
• Mapbender (PHP based mapviewing tool) (cvs) (ml) (forum)
• GpsDrive (GTK+ based geographical navigation client, which processes the GPS data provided from a NMEA capable GPS receiver, on a zoomable map. Speech output is supported trough "Festival".) (ml)
• NavSys (GTK+ based navigation and multimedia application) (cvs)
• MapEditor (GTK+ based tool to draw maps generated by NavSys) (cvs)
• Cumulus (Qtopia based mapviewing tool) (ml)
• Viking (GTK+ based data manager)
• tgpsd (Server software which interfaces directly to a NMEA capable GPS reviever to provide local and remote tcp clients with position/time data)
• GPS3D (Collection of utilities to manipulate and visualize 3D GPS data. License: none, it is public domain.)
• GPSBabel (Tool to read and write GPS waypoints in a variety of forms. Supported formats include: GPX, Magellan and Garmin serial protocols, Geocaching.com *.loc, GPSMan, Garmin Mapsource *.mps, Magellan Mapsend *.wpt, and many others.) (cvs) (ml)
• GPSTk ("GPS Toolkit". C++ library with GPS/navigation related functions.) (ml)
• GPSMan (Tcl-Tk GUI/command-line based GPS data manager)
• MagCon (Palm PDA tool to read tracks from a Magellan GPS device)
• gpspoint (Tool to download and upload, waypoints, routes and tracks from/to a Garmin GPS device)
• GPS Manager (Qt based GUI for organising GPS data using gpspoint) (cvs)
• RoadMap (GTK+ based street map viewer, which can interface with a GPS device. Inactive project.)

- GIS Portals

• FreeGIS (Portal for free GIS software and geo-data) (ml)
• OpenSourceGIS (Portal for free GIS software and geo-data)
• RemoteSensing.org (Remote Sensing related free software projects) (projects)

- GIS Components

• GDAL ("Geospatial Data Abstraction Library". C++ library for reading and/or writing of several raster file formats) (cvs) (ml)
• PostGIS (PostgreSQL database extensions for using geographical objects)
• GPLIGC (Perl based tool to analyse and visualize flight path data in the IGC format)
• GMT ("Generic Mapping Tools". Collection of about 60 tools that allow users to manipulate x,y and x,y,z data sets.)
• OpenLayers (JS library for displaying map data in web browsers) (ml)
• FeatureServer (RESTful geographic feature service) (ml)
• Mapbuilder (Javascript based mapping widgets) (cvs) (ml)
• Mapbender (PHP/Javascript based mapping widget)

- GIS Solutions

• Mapstraction (JS based library which provides a common API for Google, Yahoo and MS mapping APIs) (svn) (ml)

Electronics

• QtDMM ("Qt Digital Multi-Meter". Tool for reading and displaying the data output of several DMM models.)

Computer Science

• Computer Science (from the Computer Science section)

Linguistics

• Text Synthesis & Recognition Tools (from the Text Management section)
• Speech Synthesis & Recognition Tools (from the Multimedia section)

History

• Gramps (GNOME based genealogy research program with GEDCOM import and export support) (cvs) (ml) (forum)
• Lifelines (Genealogy research program with support for scriptable reporting and reading/writing of the GEDCOM file format. License: BSD-style) (cvs) (ml)

Economics

• Gretl (Gnu Regression, Econometrics and Time-series Library. C based library with functions relating to econometric estimation. Gretl includes a command-line client program and a GNOME client) (cvs) (ml)