Portal:FLOSS4Science/Featured/more

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=

=Unclassified=

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.

=Generic=

Data mining

 * Data Mining (book)
 * Resources

Maths and Stats

 * MATH - OpenOffice.org's component for mathematical equations.
 * OOo Statistics
 * JMathLib
 * Agros2D - solving partial differential equations.
 * PSPP - a program for statistical analysis of sampled data.
 * gretl - Gnu Regression, Econometrics and Time-series Library.

Plotting

 * Ctioga
 * Approximatrix - (not really science oriented).
 * gnuplot - a portable command-line driven graphing utility for various platforms.

See Charting above.

General

 * NIST's Guide to Available Mathematical Software (GAMS)
 * Math, Statistics, and Computational Science
 * Other sources

Lists

 * Open Directory Project
 * Software for mindmapping and information organisation

Grid and Cluster Computing

 * Beowulf
 * FAQ
 * BOINC
 * BOINC Stats
 * Clustering routines that can be used to analyze gene expression data
 * and clustering methods for gene expression data analysis
 * Gluster - a GNU clustering platform
 * Grid Engineand wiki.
 * The High Availability Linux project
 * HeartBeat
 * 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.
 * OpenSSI
 * OSCAR
 * 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)
 * project web site

=Field/discipline-specific=

Bioinformatics

 * Bio-Linux

Molecular biology

 * See the applications listed on BioKnoppix

Chemistry

 * Kalzium - explore the periodic table]
 * Gnome Chemistry Utils
 * Linux4Chemistry
 * 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.

Astronomy

 * Stellarium
 * Celestia
 * KStars
 * Aladin


 * List

GIS and Spatial Analytical Tools
Suggestion: categorise as Viewer, Intermediate Spatial Analysis Tool, or Advanced Spatial Analysis Tool. See also: List of geographic information systems software.

Comparisons

 * Overview
 * Functionality

Links

 * Free Geography Tools
 * Free GIS
 * GNU/Linux Live CD for Free and Open Source GIS applications

Data

 * Natural Resources Database - GIS

Imaging

 * (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.
 * See National Alliance for Medical Image Computing and wiki.
 * OpenDICOM
 * Aeskulap
 * kradview

Physics

 * 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.

Lists
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:


 * List of computer simulation software
 * List of system dynamics software
 * Simulation software development frameworks
 * Simulation application software
 * List of discrete event simulation software

General
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
 * Spreadsheets
 * OpenOffice.org - Calc
 * Gnumeric

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

=etc.=


 * 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.