Advanced Topic: Automation

cytoscape.github.io/cytoscape-tutorials/presentations/advanced-automation-2018-ucsf.html


Gladstone/UCSF/CCMI/CZ Biohub

26 June 2018

Goals and Motivations

By the end of this workshop you should be able to:
  • Know when and how to use Cytoscape
  • Identify relevant types and sources of networks
  • Command programmatic control over Cytoscape
  • Integrate Cytoscape into your bioinformatics pipelines
  • Publish, share and export networks online
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Cytoscape Automation

Introductions

John "Scooter" Morris, UCSF
  • Adjunct Assistant Prof, Pharmaceutical Chemistry
  • Executive Director RBVI
  • Cytoscape team since 2006
  • Author of over a dozen Cytoscape apps
Alex Pico, Gladstone Inst.
  • Associate Director, Bioinformatics
  • Executive Director NRNB
  • Cytoscape team since 2006
  • Author of half a dozen Cytoscape apps

Introductions

What about you?

  • Clinicians
  • Bench Biologists
  • Bioinformaticians
  • Computer Scientists
  • Chemists
  • Mathematicians
  • Other

Introductions

Cytoscape/Network Analysis experience?

  • None -- that's what I'm here for!
  • Some network analysis, but what's Cytoscape?
  • I've played with Cytoscape, but still have a lot to learn.
  • I do a lot with networks, but mostly in R/Python/Matlab/...
  • I do all of the above...
    (hey, I could probably teach this course!)

Tour of Cytoscape


  1. Launch Cytoscape v3.6.1

Tour of Cytoscape


  1. Open CyBrowser
  2. Enter URL: tutorials.cytoscape.org

Tour of Cytoscape


  1. Click on Tour of Cytoscape
  2. Resize window to your preference
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Cytoscape Automation
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Cytoscape Automation
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Cytoscape Automation

Thank You!

Here are additional resources you may find useful:

Thank You!




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