From Wikiversity

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 :-).

Contents 1 Previously Featured 2 Unclassified 3 Generic 3.1 Charting 3.2 Data mining 3.3 Maths and Stats 3.3.1 Plotting 3.3.2 General 3.4 Mindmapping 3.4.1 Lists 3.5 Grid and Cluster Computing 3.5.1 Reviews, Surveys, Lists, Communities, etc. 4 Field/discipline-specific 4.1 Biology 4.2 Chemistry 4.3 Astronomy 4.4 Geneology 4.5 GIS and Spatial Analytical Tools 4.5.1 Desktop GISs 4.5.1.1 Comparisons 4.5.1.2 Links 4.5.2 Data 4.6 Medicine 4.6.1 Imaging 4.7 Molecular biology 4.8 Physics 5 etc. 6 Developer Tools

[edit] 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

[edit] Unclassified

If you have time, please move these and expand. Thanks :-)

• Nano Hive
• Hadoop! - platform that lets one easily write and run applications that process vast amounts of data.
• TiLP - a linking program for Texas Instruments' graphing calculators.
• wxMaxima - Computer Algebra System
• Scilab - numerical computation.
• Xmgrace - WYSIWYG 2D plotting tool.
• Xfig - drawing
• LINPACK - a collection of Fortran subroutines that analyze and solve linear equations and linear least-squares problems.
• BLAST - (Basic Local Alignment Search Tool) aligns biological sequences locally and rapidly using heuristic techniques to speed the search.
• NIH ImageJ - image processing and analysis - biological images.
• List from OpenWetWare - including molecular biology, biotechnology, etc.

[edit] Generic

[edit] 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

[edit] Data mining

• Data Mining (book)
  • Resources

[edit] Maths and Stats

• MATH - OpenOffice.org's component for mathematical equations.
• OOo Statistics
• JMathLib

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.	...

[edit] Plotting

• Ctioga
• Approximatrix - (not really science oriented).

See Charting above.

[edit] General

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

[edit] Mindmapping

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

[edit] Lists

• Open Directory Project
• Software for mindmapping and information organisation

[edit] 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)

[edit] 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

[edit] Field/discipline-specific

[edit] Biology

• ....

[edit] Chemistry

• Kalzium - explore the periodic table]
• Gnome Chemistry Utils
• Linux4Chemistry

[edit] Astronomy

[edit] Geneology

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

[edit] GIS and Spatial Analytical Tools

Suggestion: categorise as Viewer, Intermediate Spatial Analysis Tool, or Advanced Spatial Analysis Tool.

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.

[edit] Desktop GISs

[edit] Comparisons

• Overview
• Functionality

[edit] Links

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

[edit] Data

• Natural Resources Database - GIS

[edit] Medicine

[edit] 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.
• 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

[edit] Molecular biology

• See the applications listed on BioKnoppix

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

[edit] Physics

• Physics Live CD - physical simulations, and software to help develop simulations.

[edit] 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.

[edit] Developer Tools

Especially where these have a slant towards some aspect of science.

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