TableOfContents

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.

• [http://www.analytictech.com/ucinet/ucinet.htm UCINET] - De facto standard network analysis tool in social science. (commercial 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.)

Layouts

• [http://apropos.icmb.utexas.edu/lgl/ LGL] - Large Graph Layout

• [http://www-sst.informatik.tu-cottbus.de/~an/GD/index.html#Downloads LinLogLayout]

• [http://www.touchGraph.com/ Touchgraph] and [http://sourceforge.net/projects/touchgraph TouchGraph]

Other link directories

• http://ihome.cuhk.edu.hk/~b400559/arraysoft_pathway.html

• http://bioinformatics.ubc.ca/resources/links_directory/?subcategory_id=82

• http://www.biochemweb.org/systems.shtml

• http://www.pathguide.org

Network Visualization

• http://www.visualcomplexity.com/vc/index.cfm

• http://www.aisee.com/