Date/Time
Date(s) - 2023-09-27 - 2023-09-29
10:00 CEST - 12:00 CEST
Categories
Network Biology: towards Cytoscape intermediate
Date: 27-29, September 2022 (3 days)
Time: 10:00 – 12:00
Location: B11 ATC + ONLINE!
Places: 12 on-site, 13 online
Cytoscape 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.
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
Course goals:
During this course participants will:
- 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
- lastly, prepare you for an advance course on Cytoscape
After the course you will be able to independently work with Cytoscape and perform some advance analysis. The course focuses on hands-on mode, i.e. the participants will be working through clearly outlined exercises. This level of understanding of Cytoscape will be beneficial when attending an advanced course on Cytoscape (tentatively towards end of this year).
Requirements:
You should have a basic idea of working with [biological] networks in Cytoscape. If you have already attended the introductory course on Cytoscape offered by CBNA previously, that would be sufficient. If not, you are advised to attend/revise the introductory course on Cytoscape offered shortly before this course.
You will need Cytoscape installed on your computer.
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)