Visualizing and Analysing Biological Networks with STRING and Cytoscape

Slides:
https://cytoscape.github.io/cytoscape-tutorials/presentations/cytoscape-and-string-2018-cpr.html

John "Scooter" Morris
Lars Juhl Jensen

Novo Nordisk Foundation Center for Protein Research
University of Copenhagen
15 November 2018

Goals and Motivations

By the end of this workshop you should be able to:

  • Understand the major applications of network biology
  • Import your data into Cytoscape
  • Master network layouts and data visualization
  • Know where to find relevant Cytoscape apps and tutorials
  • Understand STRING and how to integrate STRING data into Cytoscape
Introductions and Concepts Introduction to Cytoscape Cytoscape & STRING Cytoscape Automation Wrap up

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

Lars Juhl Jensen, CPR
  • Group leader, Cellular Network Biology @ CPR
  • Member of the STRING team since 2003
  • PI of the COMPARTMENTS, TISSUES, and DISEASES databases
  • Developer of the underlying text-mining software

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!)
Introductions and Concepts Introduction to Cytoscape Cytoscape & STRING Cytoscape Automation Wrap up

Tour of Cytoscape


  1. Launch Cytoscape v3.7.0

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

Hands-on Exercises

Recommended Exercises:

  1. Basic Data Visualization
  2. StringApp
  3. Functional Enrichment

Other tutorials are available at: tutorials.cytoscape.org

Introductions and Concepts Introduction to Cytoscape Cytoscape & STRING Cytoscape Automation Wrap up

Introduction to STRING

Cytoscape & STRING

Introductions and Concepts Introduction to Cytoscape Cytoscape & STRING Cytoscape Automation Wrap up
Introductions and Concepts Introduction to Cytoscape Cytoscape & STRING Cytoscape Automation Wrap up

Wrap up

Questions and Discussion

Thank You!

Here are additional resources you may find useful:

Thank You!




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