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Scientific Software

Table of Contents

  1. Scientific Publication Portals
  2. 'Free-for-non-commercial-use'
    Scientific Publication Portals
  3. Scientific Software Portals (non-specific)
  4. Data Management Tools
  5. Plotting & Graphing Tools
  6. Numerical and Algorithmic Tools
  7. Technical Process Analysis & Simulation
  8. Natural Process Analysis & Simulation

    (not chemistry/biology/astronomy specific)

  9. Chemistry
  10. Biology
  11. Astronomy
  12. Geospatial Science
  13. Electronics
  14. Computer Science (from the Computer
    Science section)
  15. Linguistics
  16. History
  17. Economics

Scientific Publication Portals

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

Scientific Software Portals (non-specific)

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
    a Perl module interface for GD)
  • Matplotlib
    (Python based library for the creation of 2D plots and graphs. License:
    Python Software Foundation)
    (cvs)
    (ml)
  • LabPlot
    (KDE based 2D/3D plot tool)
  • Guppi
    (GNOME based 2D/3D plot tool)
    (ml)
  • Cug
    (GTK+ based 2D/3D plot tool)
  • RLPlot
    (Qt based interactive 2D plotting tool)
    (cvs)
  • Ploticus
    (Flexible command-line tool to create 2D plots and graphs.
    Inactive project.)
    (forum)
  • 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)
  • 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

- Spreadsheet Tools

- Desktop Calculators

- Numerical and Algorithmic Frameworks

  • Gnu Octave
    (High-level interactive language for numerical computations)
    (cvs)
    (ml)
  • 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)
  • 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)
  • 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".)
  • 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)
  • 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

  • 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.)
  • FreeGIS Geo Data links
  • OpenStreetMap
    (Initiative to create free street maps)
    (ml)
  • 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: ?

- GPS Tools

  • 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)
  • 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

- 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.)

- GIS Solutions

  • Earth3D
    (Qt based, interactive tool for rendering the earth-maps in a 3D view)
    (cvs)
  • QGIS (Qt based GIS system)
    (cvs)
    (ml)
  • GRASS GIS
    (X/Tcl-Tk based GIS system)
    (GRASS/Qt
    C++ library for using GRASS functionality via a Qt GUI based application)
    (cvs)
    (ml)
  • Quantum GIS
    (Qt/PostgreSQL/PostGIS based GIS system)
    (cvs)
    (ml)
  • Thuban
    (Python/wxWidgets based geographic data viewer)
    (cvs)
    (ml)
  • Tiger Map Server
    (Web based raster-image map server with a build-in web server and GPS
    interfacing support)
  • MapServer
    (Web based tool set for building spatially enabled Internet applications)
    (ml)
  • K-Track (KDE based satellite
    prediction software which uses the NORAD SGP4/SDP4 calculation models.
    K-Track is especially suited for radio amateurs operating through the satellites
    that are providing linear transponders)
    (cvs)
  • KFLog

    (KDE based tool to analyse and visualize flight path data)

Electronics

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

Computer Science

Linguistics

History

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)
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