Network analysis and visualization with Cytoscape and STRING

The workshop assumes that participants are already familiar with STRING, i.e. that they have participated the keynote on the first day. At the workshop, I will first give a crash course on Cytoscape, a general tool for analysis and visualization of networks (not only protein networks). Afterwards, I will introduce the Cytoscape stringApp, which provides much of the functionality of the STRING web resource within the Cytoscape framework. The hands-on exercises will teach the participants how address the following tasks using Cytoscape and STRING:
  • retrieve networks for proteins or small-molecule compounds of interest
  • retrieve networks for a disease or an arbitrary topics in PubMed
  • layout and visually style the resulting networks
  • import external data and map them onto a network
  • perform enrichment analyses and visualize the results
  • merge and compare networks
  • select proteins by attributes
  • identify functional modules through network clustering
The training material for the hands-on exercises can be found here:
Participants are strongly encouraged to install all the software listed under "Prerequisites" before showing up for the workshop, both to save time and to not risk overloading the internet connection of the conference venue.