Network Biology Workflows with Cytoscape and NDEx:
Visualization, Analysis, Sharing, Automation, and Apps

Slides: https://cytoscape.org/cytoscape-tutorials/presentations/intro-cytoscape-2026-ismb.html


Chris Churas, Jing Chen, John "Scooter" Morris

UCSD and UCSF (retired)
12 July 2026
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Visualization Hands-on Exercises

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!)

Tour of Cytoscape

Follow-along walkthrough:

  1. Loading networks
  2. Loading tables
  3. Selection and filtering
  4. Changing visual attributes
  5. Exporting images
  6. Saving sessions
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Visualization Hands-on Exercises
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Visualization Hands-on Exercises
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Visualization Hands-on Exercises

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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?
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Visualization Hands-on Exercises

Working with Your Data

Take the rest of the time to use Cytoscape on your own data, or one of the additional exercises below, and to put into practice what you've just learned


Additional Exercises per Interest:

  1. Differential Expression and Omics data
  2. Proteomics and AP-MS data
  3. Cancer Genetics and variant data

Other tutorials are available at: tutorials.cytoscape.org

Thank You!

Here are additional resources you may find useful:

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