Cytoscape Wiki
International Conference on Systems Biology Demos
Description
This is an internal wiki page for collecting abstracts, data, posters, and other materials for the arena demos on Cytoscape at the International Conference on Systems Biology.
Facts on the conference and demos
- Started 2000 by Kitano, now organized by ISSB
- Lots of big names in bioinformatics
- Cytoscape will have an arena (booth) in the conference exhibition/poster area
web site: http://www.icsb-2008.org
- Arena hours: Three days: Sun Aug 24th – Tue 26th
- Aug 24 1300-1600 and 1800-2000
- Aug 25 1300-1500
- Aug 26 1300-1600 and 1800-200
- 5-10 workflows using plugins
Abstracts
Setup for abstracts
- Short abstract
- Analysis keywords
- Cytoscape keywords
- Sample and info on wiki page…
List of Abstracts
Map of Plugins to Scenarios
Use Case |
Biological Example |
Plugins |
Remarks |
Display molecular data in biological context |
Overlay Gene Expression Data on Network |
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Predict molecular interactions |
?? |
talk with David States about this |
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finding targets in cardiovascular disease |
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Find active regions |
Statistics to infer gene targets for wetlab testing |
R2AndCytoscape, McodePlugin, BiNGO? |
R2AndCytoscape is good example of how easy it is to write plugins. |
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Find possible complexes, protein families, functional relationships |
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epistatic mapping |
get epistatic map network from Scooter, break it into a separate use scenario? |
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Multi-level Network Analysis |
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Structure and Function |
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will require some familiarization with Chimera. Perhaps hook up with SubGeneViewer (splice variation to domain)? Side benefit is to show how plugins written completely independently can interoperate with each other to answer a biological question. |
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Pathway Curation, Storing and Exporting Images |
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Map of Plugins to Deliverables
Plugin / Scenario |
Who |
Abstract |
Data |
Webstart |
Video |
Comments |
AllanK |
done |
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Piet |
done |
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Scooter |
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Scooter |
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Gary |
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David |
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AllanK |
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Thomas |
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Matthias |
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Dorothea |
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Mario |
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Gang |
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Alex |
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Shoshana |
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Data
put data files here
Posters
put posters here
Presentation Guides
for each presentation, plut some powerpoint slide that describes it plus a set of scripted steps
Other stuff
Posters from ISMB
Notes
ask about GenePro, validation to gold standard, pie nodes (U toronto)
also Brian Turner's metabolomics work (same research group, Shoshana Wodak's)