Cytoscape and Network Biology:
an Introduction

Slides: http://tutorials.cytoscape.org


John "Scooter" Morris, Alex Pico and Yihang Xin

Online
24 October 2024

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 and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Q&A and What's Next

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

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 three dozen Cytoscape apps

Introductions

What about you?

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


  1. Launch the latest version of Cytoscape

Tour of Cytoscape

Follow-along walkthrough:

  1. User interface
  2. Loading networks
  3. Loading tables
  4. Selection and filtering
  5. Changing visual attributes
  6. Exporting images
  7. Saving sessions
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Q&A and What's Next
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Q&A and What's Next
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Q&A and What's Next

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 Analysis and Viz Hands-on Exercises Q&A and What's Next

What's Next

Cytoscape Web

  • Cytoscape Web is a web-based network visualization tool.
  • It allows you to visualize, analyze, and explore networks directly in the browser.
  • It directly connect to the NDEx network repository. Easier to share networks online.
  • Now, it provides "basic" network analysis... Have large networks, long workflows, or specific needs? Still use Cytoscape desktop!

What's Next

Other workshops

Q&A

Any questions?

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:

Thank You!




surveymonkey.com/r/bioinfo-training