Cytoscape and Network Biology:
an Introduction

Slides: http://tutorials.cytoscape.org


John "Scooter" Morris and Alex Pico

UCSF
12 February 2020

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 Working with Your Data

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 a handful of Cytoscape apps and RCy3

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


  1. Open CyBrowser
  2. Enter URL: tutorials.cytoscape.org

Tour of Cytoscape


  1. Click on Tour of Cytoscape
  2. Resize window to your preference

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 Analysis and Viz Hands-on Exercises Working with Your Data
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Working with Your Data
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Working with Your Data

Hands-on Exercises

Recommended Exercise for Everyone: Basic Data Visualization


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

Hands-on Exercises


What have we learned?
Introductions and Concepts Guided Tour of Cytoscape Finding Network Data Network Analysis and Viz Hands-on Exercises Working with Your Data

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:

Thank You!




surveymonkey.com/r/cytoscape