#acl All:read = 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''': 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]]