Presented by the Host Pathogen Mapping Initiative & Cancer Cell Map Initiative, this event is scheduled for May 21, 2024, at the UCSF Mission Bay campus in San Francisco, CA. No prior experience is required to participate.
The session will cover fundamental Cytoscape functionality on both desktop and web platforms from 10:00 AM to 2:30 PM. Following this, there will be an informal hands-on exploration of the ecosystem from 3:00 PM to 5:00 PM.
Draft Agenda:
Morning 10-12
- 10:00 -10:15 Brief overview of the Cytoscape Ecosystem.
- 10:15-10:30 Create your NDEx account.
- 10:30-12:00 Cytoscape tutorial, on both the desktop and the web.
- Create a network from tabular data.
- Get a network from NDEx.
- Get a network subgraph using NDEx IQuery
- Merge networks.
- Save your new networks to NDEx.
Lunch 12-1
Afternoon 1-5
- 1:00-1:30 Apply visual styles and layouts to the networks.
- 2:00-2:30 Save the updated networks to NDEx, try the “open in Cytoscape” NDEx feature
- 2:30-3:00 Catch up, break.
- 3:00-4:00 Quick intro to:
- NDEx network queries.
- CDAPS: building hierarchical models via multi-scale network clustering.
- HiView mode to visualize hierarchical models.
- Experimental LLM gene set query feature.
- 4:00-5:00 Experimentation with help from the instructors.
