Department of Bioinformatics – BiGCaT

Cytoscape automation workshop

Date:24th of November 2017
Location: Maastricht, NL

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.
Please register here.

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

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


Alexander Pico 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 in San Francisco, CA. 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.


Morning session (09:30-12:30)
09:30-10:00 Introductions to network biology and Cytoscape
10:00-10:30 Finding and assessing types of networks, sources, and relevant apps
10:30-11:00 Break
11:00-12:00 Network visualization: data overlays & layouts
12:00-12:30 Network analysis: topological & data-driven

Lunch (12:30-13:30)

Afternoon session  (13:30-16:30)
13:30-14:00 Overview of Cytoscape Automation and setup
14:00-14:30 Loading disease network into Cytoscape via R
14:30-15:00 Coffee Break
15:00-16:30 Interacting with Cytoscape
– CyREST, Commands and r2cytoscape package
– Visualizing data on networks
– Loading multiple data types into Cytoscape
– Setting visual styles
– Subnetwork selection
– Data-driven and diffusion-based subnetworks
– Saving, sharing and publishing

Additional Topics and Q&A (16:30-17:00)