CCMI - Presentation

UCSF - Cytoscape Automation in R and Python for Bioinformaticians



1:00 PM-5:00 PM

Discover the new capabilities of Cytoscape using R and Python.

Slides for the workshop are available for download here!

Cytoscape is one of the most popular applications for network analysis and visualization. In this workshop, we will demonstrate new capabilities to integrate Cytoscape into programmatic workflows and pipelines using R and Python. We will begin with an overview of network biology themes and concepts, and then we will translate these into Cytoscape terms for practical applications. The bulk of the workshop will be a hands-on demonstration of accessing and controlling Cytoscape from R and Python to perform a network analysis of tumor expression and variant data.

By the end of tutorial, you should be able to

  • Know when and how to use Cytoscape in your research area
  • Identify and discriminate relevant source of interactions, networks and datasets
  • Command programmatic control over Cytoscape
  • Integrate Cytoscape into your bioinformatics pipelines
  • Publish, share and export networks
  • Generalize network analysis methods to multiple problem domains

This tutorial is intended for an audience that has prior experience with at least one of the following:

  • Network visualization using Cytoscape
  • Bioinformatics analysis using R or Python

Participants are required to bring a laptop with Cytoscape, R, RStudio and Python 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.

Adam Treister, Gladstone Institutes. Adam is a senior software engineer with core, app, and automation development experience. At the Bioinformatics core at the Gladstone Institutes, he performs software design and implementation for Network Biology applications, primarily around Cytoscape in its myriad forms.

Co-Hosted By

Gladstone Bioinformatics Core and CCMI

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.

Pictures of Scientists Having Fun

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