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EMBL-EBI: Network analysis with Cytoscape and PSICQUIC




This workshop will guide novice users through the process of analysing interaction networks – that allow biologists to map and characterise signalling pathways and to predict the function of unknown proteins.

It will use practical examples in the popular open-source tool Cytoscape and the PSICQUIC client to access several protein interaction repositories at the same time to integrate protein data from different sources. Data from external sources will then be incorporated using different Cytoscape apps to perform clustering and GO enrichment analysis over our newly created networks.



Pablo Porras Millan, EMBL-EBI


Audience and Prerequisites

  • The workshop is aimed to biologists or computer scientists with little or no previous knowledge of Cytoscape
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals


Syllabus, Tools and Resources

During this course you will learn about:

  • Molecular interaction network analysis
  • PSICQUIC and molecular interaction data integration
  • Basic principles of network analysis
  • Basic Cytoscape functionality and use of apps for clustering and GO enrichment analysis


Learning Objectives

After this course you should be able to:

  • Understand how the PSICQUIC client can help you to integrate molecular interaction data from different public repositories
  • Utilise a range of Cytoscape apps to generate and analyse interaction networks



Book Here



09:30 - 10:30 Introduction to PSICQUIC and MI data integration Pablo Porras Millan
10:30 - 11:00 Introduction to network analysis and Cytoscape Pablo Porras Millan
11:00 - 11:15 Tea/Coffee break
11:15 - 12:30 Cytoscape basics (hands-on) Pablo Porras Millan
12:30 - 13:30 Lunch
13:30 - 15:00 Cytoscape basics (hands-on) Pablo Porras Millan
15:00 - 15:15 Tea/Coffee break
15:15 - 17:00 Cytoscape basics (hands-on) cont'd  
17:00 End of workshop
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