Network Biology: Cytoscape in practice

Date: 25-26, Jauary 2024 (2 days)
Time: 14:00 – 16:00
Location: Seminar room 1-100 (Biocomputin Seminar room) + ONLINE!
Places: 12 on-site, 13 online

You

• wish to learn working with networks via a graphical user interface?
• already know the basics of Cytoscape and wish to deepen this skill?
• wish to practise Cytoscape through biological use case scenarios?

then this workshop on biological network visualization using Cytoscape might be the right choice for you.

Cytoscape is a multi-platform open-source tool for visualising interaction networks and integrating them with annotations, multi-omic profiles and other state data.

Host-Virus protein interactions

Alzheimer disease protein-protein interaction network

UMAP plot of single cell rna-seq data in Cytoscape

Differential gene expression visualization

Cholesterol pathway and drug interaction

Visualizing AP-MS data

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Course contents:

Specifically, the participants will try following biological use cases:

• learn making stringApp queries, for obtaining networks of genes, diseases, etc
• explore virus-host interaction network and functional enrichment
• work with visualizing differential expression over a netowrk and enrichment analysis
• make pathway via WikiPathways and adding drug-targets to pathway using CyTargetLinker.
• explore working with affinity purification mass spec data (AP-MS) via stringApp and EnhancedGraphics
• working with single cell RNA-seq data in Cytoscape using scNetViz

The exercises will also equip participants for being able to independently work with Cytoscape and perform some advance analyses.

The course focuses on hands-on mode, and the participants will be working on clearly outlined documented exercises.

Furthermor, this level of understanding of Cytoscape will be beneficial when attending an advanced course on Cytoscape (tentatively soon).

Requirements:

• You have an interest in gaining the skill of network science and apply it to your research topic and you are willing to explore it.
• Elementary idea of network
• You will need Cytoscape installed on your computer. (It is easy… just follow the link, download and install!)

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 courses in the series:

• Cytoscape introductory/beginners: Basic concepts, visualization, file-formats, exploring netowrks, filteration, networks measures etc.
• Cytoscape advance (tentatively end of this year). Programatic access to Cytoscape via Python and R.

Best wishes
Santhust
(santhust@embl.de)

Bookings