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
- 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
- Adjunct Assistant Prof, Pharmaceutical Chemistry
- Executive Director RBVI
- Cytoscape team since 2006
- Author of over a dozen Cytoscape apps
- Associate Director, Bioinformatics
- Executive Director NRNB
- Cytoscape team since 2006
- Author of half a dozen Cytoscape apps
Introductions
- Clinicians
- Bench Biologists
- Bioinformaticians
- Computer Scientists
- Chemists
- Mathematicians
- Other
Introductions
- 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
- Launch Cytoscape v3.6.1
Tour of Cytoscape
- Open CyBrowser
- Enter URL: tutorials.cytoscape.org
Tour of Cytoscape
- Click on Tour of Cytoscape
- Resize window to your preference