At this stage, we need a list of FLOSS for Science. Please add - even just a name and a link ... or links to other sites with lists. If you have time and feel inclined, feel free to redesign this page. Thanks :-).
Previously Featured 
|FLOSS||Type of Users||Description||URL||Links|
|Science-oriented distros||Scientists||Complete free operating systems for scientists||various||SL, ...|
|GNU Octave||Scientists doing numerical computation||A high-level language, primarily intended for numerical computations||Octave home||FAQ, Docs,...|
|The R Project||Researchers needing statistical software||A free software environment for statistical computing and graphics||Home||FAQs|
If you have time, please move these and expand. Thanks :-)
- BLAST - (Basic Local Alignment Search Tool) aligns biological sequences locally and rapidly using heuristic techniques to speed the search.
- Hadoop! - platform that lets one easily write and run applications that process vast amounts of data.
- LINPACK - a collection of Fortran subroutines that analyze and solve linear equations and linear least-squares problems.
- List from OpenWetWare - including molecular biology, biotechnology, etc.
- Nano Hive
- NIH ImageJ - image processing and analysis - biological images.
- openDesktop.org - click on Scientific.
- Scilab - numerical computation.
- TiLP - a linking program for Texas Instruments' graphing calculators.
- Weft QDA - tool to assist in the analysis of textual data such as interview transcripts, written texts and fieldnotes.
- wxMaxima - Computer Algebra System
- Xfig - drawing
- Xmgrace - WYSIWYG 2D plotting tool.
- Science-oriented distros on DistroWatch.
|JFreeChart||Charting application with a wide range of charts.||Consider integrating with OpenOffice.org (Calc/ Base) and/or Kexi, etc.||8/10|
|KChart||Charting application for KDE||Please test this ... also under Gnome.||0|
|Open Source Charting & Reporting Tools in Java||A list including JFreeChart and jCharts||JFreeChart seems most comprehensive - check out the samples.||8/10|
Data mining 
- MATH - OpenOffice.org's component for mathematical equations.
- OOo Statistics
- Agros2D - solving partial differential equations.
- PSPP - a program for statistical analysis of sampled data.
- gretl - Gnu Regression, Econometrics and Time-series Library.
|Octave||A high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. It may also be used as a batch-oriented language. See also: Octave Integration.||Highly regarded widely!||8/10|
|R||A free software environment for statistical computing and graphics.||Highly regarded widely!||8/10|
|CALCULIX||Three-Dimensional Structural Finite Element Program - designed to solve field problems.||...||0/10|
|SAGE||Open Source Mathematics Software||Blog post|
|RGnumeric||Plugin enabling R functions to be called via R commands and used like buit-in GNumeric functions.||...|
- Approximatrix - (not really science oriented).
- gnuplot - a portable command-line driven graphing utility for various platforms.
See Charting above.
- NIST's Guide to Available Mathematical Software (GAMS)
Grid and Cluster Computing 
- Clustering routines that can be used to analyze gene expression data
- Gluster - a GNU clustering platform
- Grid Engineand wiki.
- The High Availability Linux project
- Kerrighed - SSI clustering package]
- openMosix - openMosix provides single-system image (SSI) clustering, which means that the distributed multiple resources present on the network appears to user applications as as single local resource.
- PVM (Parallel Virtual Machine)
Reviews, Surveys, Lists, Communities, etc. 
- A survey of open source cluster management systems (Linux.com 2006)
- Grid computing (Wikipedia)
- Enabling Grids for E-sciencE (Wikipedia)
Molecular biology 
- Kalzium - explore the periodic table]
- Gnome Chemistry Utils
- SHELX - a set of programs for crystal structure determination from single-crystal diffraction data.
- Spresso - Stanford Public Release Electrophoretic Separation Solver: simulation of non-linear electrophoresis (Stanford Microfluidics Laboratory).
- Jmol - an open-source Java viewer for chemical structures in 3D.
GIS and Spatial Analytical Tools 
Suggestion: categorise as Viewer, Intermediate Spatial Analysis Tool, or Advanced Spatial Analysis Tool. See also: w:List of geographic information systems software.
||Not quite Spatial Analyst, but getting there||7/10|
|QGIS||supports vector, raster, and database formats.||5/10|
|Open Source GIS||List||Many useful spatial viewing, analysis and manipulation tools.||8/10|
|Free GIS||List of FreeGIS software packages||...||4/10|
|OSSIM||Remote sensing/ image processing/ GIS package||...||0/10|
|SAGA GIS||A free geographic information system (GIS), with a special 'Application Programming Interface' (API) for geographic data processing||The SAGA API supports grid data, vector data, and tables.||...|
|GeOxygene||An open framework which implements OGC/ISO specifications for the development and deployment of geographic (GIS) applications||...|
|Thuban||An interactive geographic data viewer||...||...|
|TreeSap||Qualitative querying GIS||Rather than specifying a query using numerical measurements ("within 5km"), English phrases are used ("near"), etc.|
Desktop GISs 
- (X)MedCon - toolkit for medical image conversion. Supported formats include: Acr/Nema 2.0, Analyze (SPM), DICOM 3.0, InterFile 3.3 and PNG.
- Ginkgo CADx
- EEG / MRI Matlab Toolbox - (requires matlab 6+)
- Slicer - biomedical computing application with built-in visualization and analysis capabilities.
- Physics Live CD - physical simulations, and software to help develop simulations.
- massXpert - mass spectrometry
Modeling and Simulation 
Some of the software listed elsewhere on this page may include modelling and simulation possibilities. For now, we just list any FLOSS with modelling and simulation capabilities which may be used for scientific applications, education and research.
If you use any software on the following lists for learning/teaching, please unpack details elsewhere on this page and add links to your learning resources etc. elsewhere on this FLOSS4Science portal:
- w:List of computer simulation software
- w:List of system dynamics software
- Simulation software development frameworks
- Simulation application software
- w:List of discrete event simulation software
The following may be used in multiple domains:
- Open CASCADE Technology, 3D modeling & numerical simulation
- Spatial Modeling Environment (SME3) - integrated environment for high performance spatial modeling
- OpenOffice.org - Calc
Domain Specific 
The following are associated with specific domains of application, though some may be applied in others with a bit of imagination:
- SkyEye - an integrated simulation environment for embedded computer systems
- OpenSimulator - a 3D Application Server for creating virtual environments
- JMCAD - a program for the modelling and simulation of complex dynamic systems
- Scientific Applications on Linux
- FLOSS list on Wikipedia - includes scientific packages
- Free Science Software on Wikipedia.
- Catalog of Free and Open Source Software for Education - including software for maths and science.
- FSF List
Developer Tools 
Especially where these have a slant towards some aspect of science.