Network Visualization with Cytoscape
https://cytoscape.github.io/cytoscape-tutorials/presentations/network-visualization.html#/
Scientific Visualization Conference
Flatiron Institute
26 October 2017
Goals and Motivations
- Identify relevant types and sources of networks
- Know about various approaches to network visualization
- Know when and how to use Cytoscape
- 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
Introductions
- Computational Biologist
- Computational Astrophysicist
- Informatician
- Computer Scientist
- Data Scientist
- Astronomer
- Physicist
- Biologist
- Other?
Introductions
- None -- that's what I'm here for...
- Some network analysis, but what's Cytoscape?
- I've played with Cytoscape, but only for figures
- I do a lot with networks, but mostly in R/Python/Matlab/...
- I do a lot with networks, and use Cytoscape occasionally
- I do a lot with networks, and use Cytoscape a lot
- Lots of both (hey, I could probabaly teach this course!)
Introductions
Caveats
- Cytoscape is primarily used in biology
- My examples (and most of my users) are biologically-related
- I'm most familiar with biological use cases
However...
Introductions
- Cytoscape is not limited to biological use cases
- Some non-biological examples:
- Modeling water systems
- Fictional star distances
- Feel free to ask questions about non-biological use cases!
Introductions
Please install Cytoscape:
Cytoscape 3.6.0 Prerelease