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Instructor-led course

Provided by: Bioinformatics

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EMBL-EBI: Network Analysis with Cytoscape (ONLINE LIVE TRAINING)


This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The course will focus on giving attendees hands-on experience in the use of one of the most commonly used open source Network Visualisation Platforms, Cytoscape. The course will also access and analyse the data through Cytoscape apps, including IntAct app.

If you do not have a University of Cambridge Raven account please book or register your interest here.

Additional information
  • Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
  • Attendance will be taken on all courses and a charge is applied for non-attendance, including for University of Cambridge students. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
  • Further details regarding eligibility criteria are available here.
Target audience
  • This workshop is aimed at researchers interested in proteins, network analysis, protein-protein interactions and related areas
  • Biologists and bioinformaticians
  • Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals

No prior experience required

Topics covered

Bioinformatics, Pathway or network analysis, Pathway or network visualisation


After this course you should be able to:

  • Utilise a range of Cytoscape apps to generate and analyse interaction networks
  • Use different analysis apps within Cytoscape: IntAct, MCODE, ClueGO
  • Import your data into Cytoscape
  • Perform network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials

During this course you will learn about:

  • Biological network representation and analysis
  • Protein-protein interactions and PPI databases introduction
  • Basic Cytoscape functionality and use of apps for access to molecular interaction data (IntAct), clustering (MCODE) and GO enrichment analysis (ClueGO)

Presentations and demonstrations


This is subject to change in line with the online training schedule.

Day 1 Topics
Session 1 Introduction: Network analysis basics, Molecular interactions and interaction databases: IntAct and Cytoscape

Comfort Break
Session 2 Cytoscape practical: Accessing interaction data through the IntAct app

Session 3 Q&A session

Day 2 Topics
Session 1 Cytoscape practical: Data integration in Cytoscape

Session 2 Cytoscape practical: Topological analysis in Cytoscape: clustering with MCODE
Comfort Break
Session 3 Cytoscape practical: Enrichment analysis in Cytoscape: ClueGO
Registration Fees
  • Free for registered University of Cambridge students
  • £ 60/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.
  • £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 120/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here

Two half day sessions


Once per year


Related courses
Specialised Research Topics

Events available