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##Add a short description of this topic. E.g. The Model API layer contains core 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. |
##Add a short description of this topic. E.g. The Model API layer contains core 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. |
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* 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 |
* 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 |
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||'''DataType''' ||'''Biological Use Case''' ||'''Plugins''' ||'''Remarks''' || ||''Gene Expression||Import and Annotate Data||SimpleGeneExpressionNatureProtocols||AtheroSclerosisDemo|| || || ||MiMiPlugin ||fill in here|| MiMiPlugin||talk with David States about this || ||''Statistics to infer gene targets for wetlab testing'' ||R2AndCytoscape||Expression Data, Transcription factor data|| R2Plugin, McodePlugin|| || ||''Identify interesting aggregations of genes and/or proteins''||Find possible complexes, protein families, functional relationships|| ??? || McodePlugin, CyOogGraphLayout, CommunityStructureGraphLayout, ClusterMakerAndEpistaticMapping|| || ||''Structure and Function''|| || ??? || StructureVizChimera|| || ||''Pathway Curation, Storing and Exportin Images''|| || ??? || WikiPathways|| || ||''Multi-level Network Analysis''|| || ||DomainGraphAndSpliceVariation, NetAnalyzer|| || |
||'''Use Case''' ||'''Biological Example''' ||'''Plugins''' ||'''Remarks''' || ||''Display molecular data in biological context'' ||Overlay Gene Expression Data on Network ||SimpleGeneExpressionNatureProtocols || ||''Predict molecular interactions''|| ?? ||MiMiPlugin ||talk with David States about this || || ||AtheroSclerosisDemo || Agilent Literature Search|| || ||''Find active regions''|| Statistics to infer gene targets for wetlab testing''|| || R2AndCytoscape, McodePlugin || || || ||Find possible complexes, protein families, functional relationships || ||McodePlugin, CyOogGraphLayout, CommunityStructureGraphLayout, ClusterMakerAndEpistaticMapping || || ||''Structure and Function'' || ||??? ||StructureVizChimera || || ||''Pathway Curation, Storing and Exportin Images'' || ||??? ||WikiPathways || || ||''Multi-level Network Analysis'' || || ||DomainGraphAndSpliceVariation, NetAnalyzer || || |
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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 |
|||
Predict molecular interactions |
?? |
talk with David States about this |
||
|
Agilent Literature Search |
|
||
Find active regions |
Statistics to infer gene targets for wetlab testing |
|
|
|
|
Find possible complexes, protein families, functional relationships |
|
McodePlugin, CyOogGraphLayout, CommunityStructureGraphLayout, ClusterMakerAndEpistaticMapping |
|
Structure and Function |
|
??? |
|
|
Pathway Curation, Storing and Exportin Images |
|
??? |
|
|
Multi-level Network Analysis |
|
|
|
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