Differences between revisions 12 and 15 (spanning 3 versions)

Software applications

[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16417636&query_hl=2&itool=pubmed_docsum GenoLink]. Free executable for academic use.
[http://ondex.sourceforge.net ONDEX]. Open source.
[http://nwb.slis.indiana.edu/ Network Workbench] A Large-Scale Network Analysis, Modeling and Visualization Toolkit for Biomedical, Social Science and Physics Research
[http://visant.bu.edu/ VisANT] - Java biological analysis software
[http://www.graphviz.org/ Graphviz] - Graph Visualization Software
[http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek] - Graph visualization and analysis software. Popular among social science community.
[http://biodata.mshri.on.ca/osprey/servlet/Index OSPREY] - Biological network visualization software.

Programming Libraries

[http://www.cytoscape.org Cytoscape] in Java. Freely available (open-source)
[https://networkx.lanl.gov/ NetworkX] in Python
[http://sbi.imim.es/piana/ PIANA] in Python. Freely available (open-source). Outputs results in Cytoscape 'importable' format (ie. sif, noa, eda).
[http://www.bioconductor.org/packages/bioc/stable/src/contrib/html/graph.html Bioconductor graph package] in R. Freely available (open-source)
[http://www.jgraph.com/ JGraph] - Java Graph Visualization and Layout
[http://www.yworks.com/en/products_yfiles_about.htm yFiles] - Java Graph Layout and Visualization Library
[http://jgrapht.sourceforge.net/ JGraphT] - Java graph library
[http://jung.sourceforge.net/team.html JUNG] - Java Universal Network/Graph Framework
[http://medcd.iab.keio.ac.jp/expanda/ eXpanda] - Perl library for network visualization and analysis. (can import Cytoscape sif files.)

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+ * [http://vlado.fmf.uni-lj.si/pub/networks/pajek/ Pajek] - Graph visualization and analysis software.  Popular among social science community.

 * [http://biodata.mshri.on.ca/osprey/servlet/Index OSPREY] - Biological network visualization software.
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+ * [http://jung.sourceforge.net/team.html JUNG] - Java Universal Network/Graph Framework

 * [http://medcd.iab.keio.ac.jp/expanda/ eXpanda] - Perl library for network visualization and analysis. (can import Cytoscape sif files.)