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||<tablewidth="" tablealign=""^>#||'''Demo/Recipes''' ||'''Network Context''' ||'''Biological Use Case''' ||'''Plugins used(abstracts)''' ||Primary ||Secondary ||'''Remarks''' || ||<^>1||NatureProtocolsDemo ||''Annotate network'' ||Overlay Gene Expression Data on Network ||jActiveModules? ||Everyone ||Everyone ||Need to get full list of plugins for this || ||<^>2||MiMiPpiDiscoveryRecipe ||''Expand network'' ||Predict molecular interactions ||MiMiPlugin ||Piet ||?? ||talk with David States about this || ||<^>3||AgilentLiteratureSearchRecipe ||''Find active regions'' ||Find probable targets in cardiovascular disease ||AtheroSclerosisDemo ||AllanK ||?? ||work in VistaClara plugin || ||<^>4||R2InferGeneTargetsRecipe || ||Infer gene targets for wetlab testing ||R2Plugin, BiNGO, NetMatch ||Piet ||?? ||R2AndCytoscape is good example of how easy it is to write plugins. || ||<^>5||McodePluginRecipe || ||Find possible complexes, protein families, functional relationships || McodePluginDemo ||Chris??|| ?? || ||<^>6|| ClusterMakerRecipe|| || ||ClusterMakerDemo||Allan||??|| || ||<^>7||CyOogGraphLayoutRecipe|| || ||CyOogGraphLayout||Mattias||??|| || ||<^>8||CommunityStructureLayoutRecipe|| || ||CommunityStructureLayout||Allan||??|| || ||<^>9||DomainGraphRecipe, NetworkAnalyzerRecipe ||''Multi-level Network Analysis'' ||Which splice variants influence the structure of ppi networks ||DomainGraph, NetworkAnalyzer ||Dorothea ||?? || || ||<^>10||StructureVizRecipe || ||Expand the network by incorporating lower level structure and function ||StructureVizDemo ||Allan ||?? ||will require some familiarization with Chimera. Perhaps show a slide about the interconnection 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. || ||<^>11||WikiPathwaysRecipe ||''Pathway Curation, Storing and Exporting Images'' ||Storing and expanding knowledge of biological networks ||WikiPathwaysPathVisio ||Thomas ||?? || || |
||<style="VERTICAL-ALIGN: top"># ||'''Demo/Recipes''' ||'''Network Context''' ||'''Biological Use Case''' ||'''Plugins used(abstracts)''' ||Primary ||Secondary ||'''Remarks''' || ||<style="VERTICAL-ALIGN: top">1 ||NatureProtocolsDemo ||''Annotate network'' ||Overlay Gene Expression Data on Network ||jActiveModules? ||Everyone ||Everyone ||Need to get full list of plugins for this || ||<style="VERTICAL-ALIGN: top">2 ||MiMiPpiDiscoveryRecipe ||''Expand network'' ||Predict molecular interactions ||MiMiPlugin ||Piet ||?? ||talk with David States about this || ||<style="VERTICAL-ALIGN: top">3 ||AgilentLiteratureSearchRecipe ||''Find active regions'' ||Find probable targets in cardiovascular disease ||AtheroSclerosisDemo ||AllanK ||?? ||work in VistaClara plugin || ||<style="VERTICAL-ALIGN: top">4 ||R2InferGeneTargetsRecipe || ||Infer gene targets for wetlab testing ||R2Plugin, BiNGO, NetMatch ||Piet ||?? ||R2AndCytoscape is good example of how easy it is to write plugins. || ||<style="VERTICAL-ALIGN: top">5 ||McodePluginRecipe || ||Find possible complexes, protein families, functional relationships ||McodePluginDemo ||Chris?? ||?? || ||<style="VERTICAL-ALIGN: top">6 ||ClusterMakerRecipe || || ||ClusterMakerDemo ||Allan ||?? || || ||<style="VERTICAL-ALIGN: top">7 ||CyOogGraphLayoutRecipe || || ||CyOogGraphLayout ||Mattias ||?? || || ||<style="VERTICAL-ALIGN: top">8 ||CommunityStructureLayoutRecipe || || ||CommunityStructureLayout ||Allan ||?? || || ||<style="VERTICAL-ALIGN: top">9 ||DomainGraphRecipe, NetworkAnalyzerRecipe ||''Multi-level Network Analysis'' ||Which splice variants influence the structure of ppi networks ||DomainGraph, NetworkAnalyzer ||Dorothea ||?? || || ||<style="VERTICAL-ALIGN: top">10 ||StructureVizRecipe || ||Expand the network by incorporating lower level structure and function ||StructureVizDemo ||Allan ||?? ||will require some familiarization with Chimera. Perhaps show a slide about the interconnection 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. || ||<style="VERTICAL-ALIGN: top">11 ||WikiPathwaysRecipe ||''Pathway Curation, Storing and Exporting Images'' ||Storing and expanding knowledge of biological networks ||WikiPathwaysPathVisio ||Thomas ||?? || || |
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||NatureProtocolsDemo ||AllanK || || || || || || || ||WikiPathwaysPathVisio ||Thomas ||done || || || || || || |
||NatureProtocolsDemo ||AllanK ||deferred || || ||deferred || ||what is in the actual paper will suffice || ||WikiPathwaysPathVisio ||Thomas ||done || || ||done || || || |
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| ||CommunityStructureLayout ||Gang || || || || || attachment:Gangview.wmv || || | ||CommunityStructureLayout ||Gang ||done || || || || attachment:Gangview.wmv || || |
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
Setup for plugin abstracts
- Short abstract
- Analysis keywords
- Cytoscape keywords
- Sample and info on wiki page…
Setup for workflow recipes
- Required
- Biological use case
- Scripted recipe describing data, plugins, cytoscape version, GUI steps to take to demo
- Datafiles
- Presentation (ppt)
- Suggested
- Out of the box webstart...
- Video (Allan; can you add sites discussed with Gang?)
Check the WorkflowRecipeTemplate to create your own
Map of Plugins to Scenarios
# |
Demo/Recipes |
Network Context |
Biological Use Case |
Plugins used(abstracts) |
Primary |
Secondary |
Remarks |
1 |
Annotate network |
Overlay Gene Expression Data on Network |
jActiveModules? |
Everyone |
Everyone |
Need to get full list of plugins for this |
|
2 |
Expand network |
Predict molecular interactions |
Piet |
?? |
talk with David States about this |
||
3 |
Find active regions |
Find probable targets in cardiovascular disease |
AllanK |
?? |
work in VistaClara plugin |
||
4 |
|
Infer gene targets for wetlab testing |
Piet |
?? |
R2AndCytoscape is good example of how easy it is to write plugins. |
||
5 |
|
Find possible complexes, protein families, functional relationships |
Chris?? |
?? |
|||
6 |
|
|
Allan |
?? |
|
||
7 |
|
|
Mattias |
?? |
|
||
8 |
|
|
Allan |
?? |
|
||
9 |
Multi-level Network Analysis |
Which splice variants influence the structure of ppi networks |
Dorothea |
?? |
|
||
10 |
|
Expand the network by incorporating lower level structure and function |
Allan |
?? |
will require some familiarization with Chimera. Perhaps show a slide about the interconnection 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. |
||
11 |
Pathway Curation, Storing and Exporting Images |
Storing and expanding knowledge of biological networks |
Thomas |
?? |
|
To Do
Plugin / Scenario |
Who |
Abstract |
Data/Session |
Webstart |
Script |
Video |
Comments |
AllanK |
done |
|
|
draft |
|
|
|
Piet |
done |
|
|
done |
|
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|
Scooter |
draft |
|
|
draft |
|
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|
Scooter |
draft |
|
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draft |
|
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Gary |
done |
|
|
|
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|
|
David, Jing |
done |
|
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draft |
from David States, at http://www.youtube.com/watch?v=R5yFOiRb18I&feature=related |
|
|
AllanK |
deferred |
|
|
deferred |
|
what is in the actual paper will suffice |
|
Thomas |
done |
|
|
done |
|
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Matthias |
|
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|
Dorothea |
done |
|
|
done |
|
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Mario |
done |
|
|
done |
|
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Gang |
done |
|
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|
attachment:Gangview.wmv |
|
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Shoshana |
|
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|
Data
put data files here
Posters
put posters here
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)
we will also be receiving a video from Alitora (http://alitora.com/index.html) about their semantic web plugin for Cytoscape.
we will need sound setup for the videos
Use Yeyejide's tutorial materials (from [http://www.cytoscape.org/cgi-bin/moin.cgi/CytoscapeRetreat2008/UserTutorial?highlight=(tutorial) http://www.cytoscape.org/cgi-bin/moin.cgi/CytoscapeRetreat2008/UserTutorial?highlight=%28tutorial%29])?
Cerebral has nice tutorial at http://www.pathogenomics.ca/cerebral/tutorials.html#1, with already worked out recipe and biological use case. Should we consider doing a demo of it?
Travel Details
Flight and hotels of participants
Name |
Arrival |
Hotel |
Piet |
Saturday 9:55 AM - KL 1153 |
|
Annette, Allan |
Friday 12:20 PM - UA 9362 |
|
Chris |
Friday morning? |
? |