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.

The timetable for this event can be found here.

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

• 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
• Further details regarding eligibility criteria are available here
• Further details regarding the charging policy are available here

Basic knowledge of interaction data resources and techniques is recommended

Number of sessions: 1

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

• Bioinformatics

• Pathway or network analysis

• Pathway or network visualisation

One full day session

A number of times per year

• EMBL-EBI: Protein Sequence Databases with UniProt
• EMBL-EBI: Interactions & Pathways - IntAct & Complex Portal
• EMBL-EBI: Interactions & Pathways - Reactome
• EMBL-EBI: Introduction to EMBL-EBI resources