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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

(See schedule below)

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	NatureProtocolsDemo	Annotate network	Overlay Gene Expression Data on Network	jActiveModules?	Everyone	Everyone	use attachment:retreat2008_tutorial.doc
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	CyOogPowerGraphAnalysisRecipe			[:CyOog:CyOogAbstract]	Matthias	??
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	??

To Do

Plugin / Scenario	Who	Abstract	Data/Session	Webstart	Script	Video	Comments
AtheroSclerosisDemo	AllanK	done			draft
R2AndCytoscape	Piet	done			done
StructureVizChimera	Scooter	draft			draft
ClusterMakerDemo	Scooter	draft			draft
McodePluginDemo	Gary	done
MiMiPluginDemo	David, Jing	done			draft	from David States, at http://www.youtube.com/watch?v=R5yFOiRb18I&feature=related
NatureProtocolsDemo	AllanK	see comments			see comments		what is in the actual paper will suffice. Use attachment:retreat2008_tutorial.doc
WikiPathwaysPathVisio	Thomas	done			done
CyOogPowerGraphAnalysis	Matthias	done	done	done	done		Plugin on website still with bug
DomainGraph	Dorothea	done			done
NetworkAnalyzer	Mario	done			done
CommunityStructureLayout	Gang	done				attachment:Gangview.wmv
WodakLabDemos	Shoshana

Data

put data files here

Posters

put posters here

Schedule

Day	Timeslot	Recipe-demo I	By	Recipe-demo II	By	Remarks
Saturday	14:00-18:00	Rehearsal	All (Doro in at 16:00)	-	-	Location to be established
""	19:00-21:00	Demo dinner	All	-	-	Location to be established
Sunday	10:00-12:00	Rehearsal	All	-	-	Location to be established
""	13:00-13:30	AtheroSclerosisDemo	Allan	NatureProtocolsDemo	Piet	Booth
""	13:30-14:00	tbd	tbd	R2InferGeneTargetsRecipe	Piet	Booth
""	14:00-14:30	tbd	tbd	tbd	Piet	Booth
""	14:30-15:30	tbd	tbd	tbd	Piet	Booth
""	13:00-13:30	tbd	tbd	NatureProtocols	Piet	Booth
""	13:00-13:30	Atherosclerosis	Allan	NatureProtocols	Piet	Booth

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 have received 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	[http://maps.google.com/maps?f=q&hl=en&geocode=&q=Norra+Hamngatan+38+Göteborg,+S-40126&sll=57.708572,11.972737&sspn=0.010432,0.027637&ie=UTF8&ll=57.708916,11.971793&spn=0.010431,0.027637&z=15&iwloc=addr Hotel Opera]
Annette, Allan	Friday 12:20 PM - UA 9362	[http://maps.google.com/maps?f=q&hl=en&geocode=&q=SODRA+HAMNGATAN+59-65+GOTHENBURG+S+401+24+SE&sll=37.0625,-95.677068&sspn=62.186014,113.203125&ie=UTF8&ll=57.708572,11.972737&spn=0.010432,0.027637&z=15&iwloc=addr Radisson SAS]

$/!\$ Edit conflict - other version:

Chris

Friday, noon-ish

[http://www.gothiatowers.com/index.asp?lang=EN&section=karta&page=karta Hotel Gothia Towers]

$/!\$ Edit conflict - your version: