#acl All:read
= Cytoscape Workshop - May 16, 2016 =

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

== How to access the internet ==
Username: GLBio2016<<BR>>
Password: ccbc16

== Computer set up ==
  '''Programs to Install''':
  1. A robust internet browser such as Chrome (Internet Explorer is not recommended). Firefox and Safari are also fine.
  1. Install Java 8 (verify that computer has java 8 installed. )
  1. Install Cytoscape 3.3.0: http://chianti.ucsd.edu/cytoscape-3.3.0/
  1. 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 ==
  * [[attachment:cytoscape_introduction.pptx|Lecture slides]]

== Cytoscape lab practical  ==
  * [[attachment:lab_practical1_data.zip|download data for exercise]]
  * Exercise can be found [[http://vps26122.vps.ovh.ca:8888/notebooks/Lab%20practical%201%20-%20how%20to%20use%20cytoscape.ipynb|here]]
    * (alternately it can also be found [[https://github.com/BaderLab/Cytoscape-workshop-docker/blob/master/notebooks/Lab%20practical%201%20-%20how%20to%20use%20cytoscape.ipynb|here]]) 
  
== EnrichmentMap: introduction to the exercise ==
  * [[attachment:enrichmentmap_introduction.pptx|Lecture slides]]

== Enrichment map practical ==
  * [[attachment:lab_practical2_data.zip|download data for exercise]]
  * Exercise can be found [[http://vps26122.vps.ovh.ca:8888/notebooks/Lab%20practical%202%20EnrichmentMap%20Hands-on%20training.ipynb|here]]
    * (alternately it can also be found [[https://github.com/BaderLab/Cytoscape-workshop-docker/blob/master/notebooks/Lab%20practical%202%20EnrichmentMap%20Hands-on%20training.ipynb|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]]