Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression  profiles and other state data.   Although Cytoscape was originally designed for  biological research, now it is a general platform for complex network analysis and  visualization.    Cytoscape core distribution provides a basic set of features  for data integration and visualization.   Additional features are available as plugins.   Plugins are available for network and molecular  profiling analyses, new layouts, additional file format support, scripting, and connection  with databases.   Plugins may be developed by anyone using the Cytoscape open API based on Java™  technology and plugin  community development is encouraged.  Most of the  plugins are freely available.

NEW THIS YEAR: We will briefly show and discuss new Cytoscape features: Custom Node Graphics and Attribute Equations.

Additional information on Cytoscape can be found on the Cytoscape home page, the Cytoscape Wiki, or Wikipedia.

Participants should bring their own laptop with an installed copy of Cytoscape (the workshop will cover installation for anyone having difficulties), as well as your own data to experiment with.  Finally, please click here to link to suggested reading before the workshop.

Tutorial: click here

Presentation Slides: click here

Contact: Keiichiro Ono, kono@nullucsd.edu

Cytoscape is funded by the National Resource for Network Biology (NRNB, an NIH Division of Biomedical Technology), Bioinformatics, and Computational Biology (BBCB) and Biomedical Technology Research Center (BTRC). NRNB is funded by grant GM103504.