Advanced Network Analysis and Visualisation in Cytoscape


 Thursday 23 Friday 24 April 2020


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Monday 14 October 2019

Application deadline: 

Friday 03 January 2020


Open application with selection


Rebecca Nicholl

Registration fee: 



The omics era of biological research requires more systemic approaches to data analysis and a move away from the single gene/protein perspective. The representation and analysis of the interactions between genes and proteins as network graphs is a fundamental tool in systems biology. However, the complexity of these networks poses significant challenges in terms of representation and deconvolution of the biological information they provide.  

Cytoscape is one of the most widely used tools for network data representation, integration and analysis. It is a completely free, open access desktop application specifically created with biological data analysis in mind. It offers powerful built-in network visualisation and analysis capabilities as well as ever-growing library of optional apps focused on specific functionalities that provide added versatility. Cytoscape can be used via its Graphical User Interface or programmatically via its CyREST API. 

This course will focus on advanced network analysis and visualisation functionalities of Cytoscape. The course will feature tutorials on advanced network data visualisation, integration of single cell data into network analysis, and computational access to Cytoscape functionalities. Additionally, there will be an introductory session to EMBL-EBI-based resources, highlighting those directly related to interaction and pathway information such as IntAct, PSICQUIC and Reactome. This will be followed by showcase where delegates will have the opportunity to meet with representatives from a variety of resources.


This is an advanced course aimed at researchers with previous experience with Cytoscape and network analysis, regardless of the specific data type. A basic understanding on how Cytoscape works is assumed and basic Cytoscape functionality will not be specifically addressed during the course. A working knowledge of R or Python is required to engage with the practical aspects of this workshop. 

Syllabus, tools and resources

During this course you will learn about:

  • IntAct, Complex Portal, Reactome and PSICQUIC, plus additional resources for data integration
  • Advanced visualisation options in Cytoscape including network sub-section highlighting, embedded graph plots, meta-node creation and handling
  • scNetViz app for interpretation of single cell RNAseq data using integration with protein interaction networks
  • CyREST for automation of Cytoscape workflows with R or Python workflows


After this course you should be able to:

  • Identify and access public data resources and tools for network analysis and data integration
  • Employ good network visualisation practices to make complex networks understandable
  • Apply advanced visualisation options in Cytoscape
  • Use scNetViz app for interpretation of single cell RNAseq data
  • Integrate Cytoscape analysis and visualisation using computational automation

Additional information

This course is organised in conjunction with the 2nd European Network Biology Conference: From Networks to Modeling. Delegates attending the conference will receive a 10% discount on the course registration fee.

The workshop includes an evening meal at the Hinxton Hall Restaurant on the Wellcome Genome campus, and breaks and lunch outside the EMBL-EBI training rooms.


Day 1 – Thursday 23 April 2020
8:00 Shuttle bus to campus  
8:45-9:00 Arrival and registration  
9:00-9:15 Welcome to the course Melissa Burke
9:15-9:45 Introduction to EMBL-EBI Melissa Burke
9:45-10:30 Network resources at EMBL-EBI EMBL-EBI Molecular Interactions Team
10:30-11:00 Break  
11:00-12:00 Flash talks from EMBL-EBI resources EMBL-EBI Resource Teams
12:00-13:30 Lunch and resource showcase All
13:30-15:00 Advanced visualisation with Cytoscape Scooter Morris
15:00-15:30 Break  
15:30-16:30 Advanced visualisation with Cytoscape Scooter Morris
16:30-17:30 scNetViz Scooter Morris
17:30 End of day  
18:30 Evening meal Hinxton Hall Restaurant
20:00 Shuttle bus to Cambridge station  
Day 2 – Friday 24 April 2020
8:00 Shuttle bus to campus  
9:00-10:30 Advanced automation with Cytoscape Scooter Morris
10:30-11:00 Break  
11:00-12:30 Advanced automation with Cytoscape (continued) Scooter Morris
12:30-12:45 Course wrap-up Melissa Burke
12:45-13:30 Lunch  
14:00 Shuttle bus to Cambridge station