Cytoscape Workshop - May 16, 2016

Network visualization and analysis with Cytoscape
Date: Monday, May 16, 2016
Time: 1:30pm-3:30pm
Location: VC 101

How to access the internet

Username: GLBio2016
Password: ccbc16

Computer set up

• Programs to Install:

• A robust internet browser such as Chrome (Internet Explorer is not recommended). Firefox and Safari are also fine.
• Install Java 8 (verify that computer has java 8 installed. )

• Install Cytoscape 3.3.0: http://chianti.ucsd.edu/cytoscape-3.3.0/

• Within the Cytoscape program, install the following Cytoscape apps.

  • From the menu bar, Apps > App manager...

  • Within all apps, Search for the following and Install:

    • EnrichmentMap

    • WordCloud

    • ClusterMaker2

    • AutoAnnotate

Network visualization using Cytoscape: Introduction

• Lecture slides

Cytoscape lab practical

• download data for exercise

• Exercise can be found here

  • (alternately it can also be found here)

EnrichmentMap: introduction to the exercise

• Lecture slides

Enrichment map practical

• download data for exercise

• Exercise can be found here

  • (alternately it can also be found here)

Links

• Git hub with docker image of workshop files can be found at https://github.com/BaderLab/Cytoscape-workshop-docker

• Jupyter instance of above notebooks is hosted at http://vps26122.vps.ovh.ca:8888/tree

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