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

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

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

Charting

Package	Overview	Comments	Rating
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

• 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.

Package	Overview	Comments	Rating
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.	...

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

Mindmapping

Package	Overview	Comments	Rating
Freemind	...	...	8/10
MindRaider	...	...

Lists

Search for List of mind mapping software on Wikipedia.

• 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

Biology

• ....

Bioinformatics

• Bio-Linux

Molecular biology

• See the applications listed on BioKnoppix

Package	Overview	Comments	Rating
...	...	...	0/10
...	...	...	0/10

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

Geneology

Package	Overview	Comments	Rating
...	...	...	0/10
...	...	...	0/10

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.

Package	Overview	Comments	Rating
GRASS	...	...	0/10
MapWindow	As an alternative desktop GIS To distribute data to others To develop and distribute custom spatial data analyses	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
GISKnoppix	...	...	0/10
MapServer	...	...	5/10
Free GIS	List of FreeGIS software packages	...	4/10
Cocoon ArcIms	...	...	0/10
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

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

Medicine

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:

• 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

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.

Package	Overview	Comments	Rating
...	...	...	0/10
...	...	...	0/10