CCMI - Workshop

UCSF - Introduction to Cytoscape and Network Biology



10:00 AM-5:00 PM

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Get introduced to network biology studies and Cytoscape concepts.

The network perspective on biology brings meaningful context to high-throughput data for exploratory analysis, interpretation, and hypothesis generation. As a free and open source tool, Cytoscape has become the most popular network visualization and analysis tool in the biological sciences. This workshop will provide a general introduction to network biology studies and Cytoscape concepts, including a hands-on session for universal data import and demonstration of a few of the over 300 freely available apps contributed by the Cytoscape developer community.

By the end of tutorial, you should be able to

  • Understand the major applications of network biology
  • Find relevant networks and pathways
  • Import your data into Cytoscape
  • Perform basic topological and other network analyses
  • Master network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials

This tutorial is intended for an audience that has no prior experience with Cytoscape. A solid background in biology and active research questions are expected. Participants are required to bring a laptop with Cytoscape installed. Installation instructions will be provided in the weeks preceding the tutorial.


Alexander Pico, Gladstone Institutes. Alex is the executive director of the National Resource for Network Biology, the vice president of the Cytoscape Consortium, and associate director of bioinformatics at Gladstone Institutes. He has been a contributing member to Cytoscape since 2006 and has led numerous Cytoscape and Network Biology workshops and mentoring programs over the past 10 years.

John “Scooter” Morris, UCSF. Scooter is the executive director of the Resource for Biocomputing, Visualization, and Informatics at UCSF, the “roving engineer” for Cytoscape, and an adjunct assistant professor of Pharmaceutical Chemistry at UCSF.  He has given numerous presentations on using and extending Cytoscape and is a Cytoscape core developer as well as the developer of over a dozen Cytoscape apps, including chemViz, structureViz, clusterMaker, and cddApp

No Show Policy

While we do not charge a fee to attend this event, these programs would not be sustainable and available to all wanting to attend, unless all registrants abide by the 48 hour cancellation notice policy. A no-show will also limit your ability to book our events in the future. Thank you in advance for your cooperation.


This workshop is part of a series of training events co-sponsored by the CCMI Outreach Core, UCSF Bakar Computational Health Sciences Institute and Gladstone Institutes.

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