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| Network visualization and analysis with Cytoscape Date: Monday, May 16, 2016 Time: 1:30pm-3:30pm Location: VC 101 |
'''Network visualization and analysis with Cytoscape'''<<BR>> Date: Monday, May 16, 2016<<BR>> Time: 1:30pm-3:30pm<<BR>> Location: VC 101<<BR>> |
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| Username: GLBio2016 | Username: GLBio2016<<BR>> |
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| Programs to Install: | '''Programs to Install''': |
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| * EnrichmentMap * WordCloud * ClusterMaker2 * AutoAnnotate |
* !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]]) |
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: ccbc2016
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
Cytoscape lab practical
EnrichmentMap: introduction to the exercise