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Wed 17 May 2017
09:30 - 17:00

Venue: Bioinformatics Training Room, Craik-Marshall Building

Provided by: Bioinformatics


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EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC

Wed 17 May 2017


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.

Please note that if you are not eligible for a University of Cambridge Raven account you will need to book by linking here.

Target audience
  • 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
  • Please be aware that these courses are only free for University of Cambridge students. All other participants will be charged a registration fee in some form. Registration fees and further details regarding the charging policy are available here
  • Further details regarding eligibility criteria are available here

Basic knowledge of interaction data resources and techniques is recommended


Number of sessions: 1

# Date Time Venue Trainer
1 Wed 17 May 2017   09:30 - 17:00 09:30 - 17:00 Bioinformatics Training Room, Craik-Marshall Building map Pablo Porras
Topics covered

Bioinformatics, Pathway or network analysis, Pathway or network visualisation


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

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

Presentations, demonstrations and practicals


Time Topics Speaker(s)
09:30 - 10:30 Introduction to PSICQUIC and MI data integration Pablo Porras Millan
10:30 - 11:00 Introduction to network analysis and Cytoscape
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) cont'd Pablo Porras Millan
15:00 - 15:15 Tea/Coffee break
15:15 - 17:00 Cytoscape basics (hands-on) cont'd Pablo Porras Millan 
17:00 End of workshop
Registration Fees
  • Free for University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 50/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 100/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

One full day session


A number of times per year

Specialised Research Topics

Booking / availability