Cytoscape and Network Biology:
an Introduction
Marshall University
27 February 2019
Goals and Motivations
By the end of this workshop you should be able to:
- Understand the major applications of network biology
- Find relevant networks and pathways
- Import your data into Cytoscape
- Perform basic topological and other network analyses
- Master network layouts and data visualization
- Know where to find relevant Cytoscape apps and tutorials
Introductions
John "Scooter" Morris, UCSF
- Executive director, Resource for Biocomputing, Visualization, and Informatics
- Roving Engineer, National Resource for Network Biology
- Cytoscape team since 2006
- Author of over a dozen Cytoscape apps
Introductions
Alex Pico, Gladstone Institutes
- Associate director, Bioinformatics Core
- Executive director, National Resource for Network Biology
- 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
Prior Cytoscape or 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 use Cytoscape all the time...
(hey, I could probably teach this course!)
Hands-on Exercises
What have we learned?
Working with Your Data
Take the rest of the time to use Cytoscape on your own data, or
one of the datasets below, and
to put into practice what you've just learned
Please ask questions!
Datasets to play with:
Thank You!
Here are additional resources you may find useful: