
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 highlevel 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 easytouse 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 RCommander GUI consists of a window containing several menus,
buttons, and information fields.

SciViewsR [GNU GPL]  SciViewsR is a suite of companion applications
that provides a Graphical User Interface (GUI) on top of the commandline
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 opensource 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 datavisualization, 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.

ECell
 ECell is a concept of constructing virtual cells on computers.

Open
Bioinformatics Foundation  The Open Bioinformatics Foundation or OBF
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 opensource 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 sixframe translation.

PyMOL
 PyMOL is a USERSPONSORED molecular visualization system on an OPENSOURCE
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 spatiallyenabled 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 GUIbased
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 commandline 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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