Cytoscape and Network Biology: an Introduction
John "Scooter" Morris, Alex Pico and Yihang Xin
UCSF and Gladstone
1 February 2022
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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
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Introductions
Alex Pico, Gladstone Institutes
Director, Bioinformatics Core
Executive director, National Resource for Network Biology
Cytoscape team since 2006
Author of a handful of Cytoscape apps and RCy3
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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
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Introductions
Yihang Xin, Gladstone Institutes
Software Engineer, Bioinformatics Core
Cytoscape team since 2020
Contributor of a handful of Cytoscape apps and RCy3
First time coteach this course...
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Introductions
What about you?
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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!)
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Hands-on Exercises
This tutorial presents a scenario of how expression and network data can be combined to tell a biological story.
RNA-seq Data Analysis
Hands-on Exercises
What have we learned?
What's Next
Other workshops
Cytoscape 3.9
Major new features:
Table styles -- can set up mappings for table columns
Improved performance for large networks
Support for edge Z order
Haystack edges
Copy/paste for annotations
Annotation and label rotation
New equations editor
Commands to create and modify annotations
Thank You!
Here are additional resources you may find useful:
4:50
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