april, 2015



Event Details

Network analysis has become an increasingly common approach for tackling complicated, large data sets. In the morning, this workshop will feature a number of speakers discussing their efforts to use network analysis to address pressing biological questions and unmet medical needs. One frequently used tool for network analysis is Cytoscape, an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and for 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. In the afternoon, the Cytoscape development team from Trey Ideker\’s lab will present a series of demonstrations and workshops covering a range of issues for both novice and advanced users.

New this year:

  • Cytoscape clinic
  • Lunchtime roundtable discussion on the emerging Cytoscape Cyberinfrastructure, which leverages Cytoscape and web-based services to enable advanced workflows and promote reproducibility.


Newin Cytoscape this year:

  • New publishing models for web-viewable networks
  • Nodes drawn as charts – a new dimension in visualization
  • Powerful REST interface enables liaison with Python, R and others
  • … and more!

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

VERY IMPORTANT: Participants should bring their own laptop with an installed copy of the latest Cytoscape (v3.2.1 — the workshop will cover installation for anyone having difficulties), as well as your own data to experiment with. Note that we’ll offer hands-on help during the Cytoscape Clinic.  Finally, please see suggested reading before the workshop. If you have questions, please contact Barry Demchak at idekerlab.bdemchak@gmail.com.


All Day (Friday)


Sanford Consortium for Regenerative Medicine

2880 Torrey Scenic Drive La Jolla, California 92037