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Network Analysis in Cytoscape: Advanced Topics

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The Donnelly Centre, Black seminar room

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Event description

Description

Open to UofT and affiliated researchers

Intended audience

The Advanced Topics tutorial is intended for an audience that has prior experience with at least one of the following:

  • Cytoscape software
  • Data integration and analytical methods
  • Network biology concepts
  • Bioinformatics analysis pipelines

Requirements: Bring your laptop with adequate power supply (some power cables will be provided). This will be hands on training.

Goals, objectives and motivations

By the end of tutorial, you should be able to:

  • Know when and how to use Cytoscape in your research area
  • Identify and discriminate relevant source of interactions, networks and datasets
  • Command programmatic control over Cytoscape
  • Integrate Cytoscape into your bioinformatics pipelines
  • Publish, share and export networks online
  • Generalize network analysis methods to multiple problem domains

Detailed schedule

noon-12:20 – Introductory (20 min)

  • Quick introductions & audience survey
  • General network biology overview
  • Cytoscape intro (consortium/history)
    • Roadmap: theme of integration/protocol
    • 3.5/3.6 features
    • Introduce tutorial protocol
      • Functional enrichment of RNA-seq data
      • Use this protocol as the context and examples for subsequent sections...

12:20-1:00 – Intermediate (40 min)

  • § Getting data
    • Types of data (networks, datasets), sources, and relevant apps
    • How to choose a network source: String, GeneMANIA, NDEx, WikiPathways
    • Network visualization overview
      • Style mappers & layouts
      • Apps: enhancedGraphics, etc
      • Network analysis overview
        • clusterMaker, BiNGO/ClueGO, etc

1:00-1:30 – Advanced (30 min)

  • R integration via CyREST
    • Start with dataset of calculated diff expression values (fold change)
    • Determine gene list
    • Launch Cytoscape from shell and connect

1:30-1:45

  • Break

1:45-3:30 – Advanced (105 min)

  • R integration via CyREST (continued)
    • Query string via CyREST
    • Inject tabular data (fold changes, p-Value) into Cytoscape and set styles, etc.
    • Explore network in Cytoscape
      • Hierarchical cluster & view heatmap
      • Play with styles and layouts
  • Exporting images and sessions
  • GSEA example through enrichment map & auto-annotate
  • Python integration via CyREST
    • Launch Cytoscape from shell and connect
    • Query String via CyREST
    • Cytoscape scripting: advanced (now with loops and args!)
    • Additional advanced topics, per time and interest:
      • Export to web and publishing
      • CyBrowser (new!)

Organizers and presenters

  • Alexander Pico is the Executive Director of the National Resource for Network Biology, the Vice President of the Cytoscape Consortium, and Associate Director of Bioinformatics at Gladstone Institutes. He has been a contributing member to Cytoscape since 2006 and has led numerous Cytoscape and Network Biology workshops and mentoring programs over the past 10 years.
  • John “Scooter” Morris is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics at UCSF, the “Roving Engineer” for Cytoscape, and an Adjunct Assistant Professor of Pharmaceutical Chemistry at UCSF. He has given numerous presentations on using and extending Cytoscape and is a Cytoscape core developer as well as the developer of over a dozen Cytoscape apps, including chemViz, structureViz, clusterMaker, and cddApp.
  • Barry Demchak is the Chief Architect of Cytoscape, Secretary/Treasurer of the Cytoscape Consortium and Project Manager in the Ideker lab at UCSD. He has been a contributing member to Cytoscape development since 2012 and has led numerous Cytoscape and Network Biology workshops and mentored projects over the past 5 years.
  • Adam Treister is a Senior Software Engineer with core, app and automation development experience. At the Bioinformatics Core at Gladstone Institutes, he performs software design and implementation for Network Biology applications, primarily around Cytoscape in its myriad forms.
  • Members of the Bader lab and Cytoscape teams will be on hand to help students: Christian Lopes, Mike Kucera, David Otasek, Ruth Isserlin
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The Donnelly Centre, Black seminar room

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