EVENT - Workshop

Visualizing and Analyzing Data With Networks and the Cytoscape Software Ecosystem

As part of its Host Pathogen and Cancer Cell Map Initiatives, the Quantitative Biosciences Institute (QBI) at UCSF will host a hands-on workshop on Tuesday, May 21, 2024 in Mission Bay, UCSF led by Dexter Pratt, Dylan Fong & Jing Chen from the Ideker Lab at UCSD.

The workshop, titled, "Visualizing and Analyzing Data With Networks and the Cytoscape Software Ecosystem" will cover the core Cytoscape functionality on both desktop and web, followed by an informal, hands-on exploration of the ecosystem.

Morning Session:

  • 10:00 -10:15 AM: Brief overview of the Cytoscape Ecosystem.
  • 10:15-10:30 AM: Create your NDEx account.
  • 10:30-12:00 PM: 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.

Afternoon Session:

  • 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.

No prior experience is required to participate.

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