Cytoscape automation workshop

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


  • Prior experience with R or Python
  • Some familiarity with Cytoscape (i.e., at least install it and play around before the workshop)

Deadline for registration is Nov 17th 2017.

Topics covered:

  • When and how to use Cytoscape in your research area
  • Relevant sources of interactions, networks and pathways
  • Programmatic control over Cytoscape
  • Integration of Cytoscape into your bioinformatics pipelines
  • How to publish, share and export networks

If you have any questions, feel free to contact Martina Summer-Kutmon (martina.kutmon (a)

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