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Instructor-led course

Provided by: Bioinformatics

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EMBL-EBI: Network Analysis with Cytoscape and PSICQUIC


This module provides an introduction to the theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to analyse large-scale datasets generated these to by techniques such as RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of Cytoscape and selected network analysis apps.

Also note: This event is part of a series of short introductions focusing on EMBL-EBI resources. If you want to learn more about these separate training events, see the Related Courses section below.

The training room is located on the first floor and there is currently no wheelchair or level access available to this level.

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

Target audience
  • This workshop is aimed at researchers interested in proteins, network analysis, protein-protein interactions and related areas
  • 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 registered 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

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
  • Use a variety of analysis apps within Cytoscape: BINGO, MCODE, ClueGO

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
9:30 - 10:30 Introduction to PSICQUIC and MI data integration
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) part 1
12:30 - 13:30 Lunch (not provided)
13:30 - 15:00 Cytoscape basics (hands-on) part 2
15:00 - 15:15 Tea/Coffee break
15:15 - 17:00 Cytoscape basics (hands on) part 3
Registration Fees
  • Free for registered University of Cambridge students
  • £ 50/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) 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



A number of times per year


Related courses

Events available