Biological networks visualization: Introduction to Cytoscape

Date: 28-30, September 2022 (3 days)
Time: 09:00 – 12:00
Location: Room-6.51b (Building: Main-Lab, Floor: 6) + ONLINE!
Places: 12 on-site, 13 online

Cytoscape (CS) is a multi-platform open-source tool for visualising interaction networks and integrating them with annotations, multi-omic profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. https://cytoscape.org/

Course goals:

During this 3- half-days preparatory course participants will learn how to:

• Effectively use the Cytoscape (CS) interface with it’s various options
• Prepare data (and various formats) for use in Cytoscape
• Load data into CS
• Manipulate nodes and edges in the network
• Visualise data on the nodes, and apply layouts

After the course you will be able to independently work with Cytoscape and perform basic network and data manipulation tasks in CS. The course focuses on hands-on mode, i.e. the participants will be trying during the course itself what they learn. This level of understanding of Cytoscape will be required for all subsequent CBNA courses in 2022,23.

For more details about the course, please see a previous version (on which this course is based upon) offered by Matt Rogon (former representative of CBNA).

Requirements:

Laptop and enthusiasm.
No prior knowledge of programing is required.
A rough idea about networks will be useful but not necessary.

This is a Level 1 introductory course, therefore no prior knowledge is required. You will need your own computer with Cytoscape installed.

Others:

If you would like to register to receive these announcements early, please send an empty message with the title ‘Subscribe’ to cbna@embl.de.

If you have further questions please don’t hesitate to contact us.

Notes:

• This course is for EMBL-all-sites only.

Related future courses in the series:

• Introduction to BioMart (mining annotation) and accessing interaction data with STRING and the universal database client in Cytoscape.

• Mining Biomedical Data – Accessing public databases for data retrieval pathways (KEGG, Reactome, NDex), drugs, and diseases.

Best wishes,
Santhust
(santhust@embl.de)

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