International Conference on Systems Biology Demos

Resulting Report

Find here a report on our findings: ICSB-report

Find here a generic poster to draw attention!: Cytoscape Eyecatcher

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

(See schedule below)

Setup for plugin abstracts

Setup for workflow recipes

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 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

Find possible complexes, protein families, functional relationships and view in biological context

ClusterMakerDemo

Allan

??

7

CyOogPowerGraphAnalysisRecipe

1. explore functional relationships 2. get sequence similarities that are otherwise hidden by low scoring from homology networks

CyOogAbstract

Matthias

??

8

CommunityStructureLayoutRecipe

find community structures in large biological networks, which may infer protein complexes and biological pathways.

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 retreat2008_tutorial.doc

WikiPathwaysPathVisio

Thomas

done

done

CyOogPowerGraphAnalysis

Matthias

done

done

done

done

DomainGraph

Dorothea

done

done

NetworkAnalyzer

Mario

done

done

CommunityStructureLayout

Gang

done

Gangview.wmv

WodakLabDemos

Shoshana

Data

put data files here

Posters

put posters here

Schedule

This is a preliminary schedule: subject to change (probably even in response to the audience?)

Day

Timeslot

Recipe-demo I

By

Recipe-demo II

By

Remarks

Sat Aug 23rd afternoon

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

Sun Aug 24th morning

10:00-12:00

Rehearsal

All

-

-

Location to be established

afternoon

13:00-13:30

AtheroSclerosisDemo

Allan

NatureProtocolsDemo

Piet

Booth

""

13:30-14:00

WikiPathwaysRecipe

Thomas

R2InferGeneTargetsRecipe

Piet

Booth

""

14:00-14:30

DomainGraphRecipe, NetworkAnalyzerRecipe

Dorothea

NatureProtocolsDemo

Allan

Booth

""

14:30-15:00

CyOogPowerGraphAnalysisRecipe

Matthias

CommunityStructureLayoutRecipe

Allan (video?)

Allan and/or Piet assist

""

15:00-15:30

ClusterMakerRecipe

Allan

NatureProtocolsDemo

Piet

Booth

""

15:30-16:00

McodePluginRecipe

Chris

MiMiPpiDiscoveryRecipe(incl video)

Piet

Booth

evening

18:00-18:30

NatureProtocolsDemo

Piet

WikiPathwaysRecipe

Thomas

Booth

""

18:30-19:00

CommunityStructureLayoutRecipe

Allan (video)

DomainGraphRecipe, NetworkAnalyzerRecipe

Dorothea

Booth

""

19:00-19:30

NatureProtocolsDemo

Thomas (Piet)

AtheroSclerosisDemo

Allan

Booth

""

19:30-20:00

McodePluginRecipe

Chris

CyOogPowerGraphAnalysisRecipe

Matthias

Booth

Mon Aug 25th afternoon

13:00-13:30

AtheroSclerosisDemo

Allan

NatureProtocolsDemo

Piet

Booth

""

13:30-14:00

WikiPathwaysRecipe

Thomas

R2InferGeneTargetsRecipe

Piet

Booth

""

14:00-14:30

DomainGraphRecipe, NetworkAnalyzerRecipe

Dorothea

NatureProtocolsDemo

Allan

Booth

""

14:30-15:00

CyOogPowerGraphAnalysisRecipe

Matthias

CommunityStructureLayoutRecipe

Allan (video?)

Allan and/or Piet assist

""

15:00-15:30

ClusterMakerRecipe

Allan

NatureProtocolsDemo

Piet

Booth

""

15:30-16:00

McodePluginRecipe

Chris

MiMiPpiDiscoveryRecipe(incl video)

Piet

Booth

Tue Aug 26th afternoon

13:00-13:30

AtheroSclerosisDemo

Allan

NatureProtocolsDemo

Piet

Booth

""

13:30-14:00

WikiPathwaysRecipe

Thomas

R2InferGeneTargetsRecipe

Piet

Booth

""

14:00-14:30

DomainGraphRecipe, NetworkAnalyzerRecipe

Dorothea

NatureProtocolsDemo

Allan

Booth

""

14:30-15:00

CyOogPowerGraphAnalysisRecipe

Matthias

CommunityStructureLayoutRecipe

Allan (video?)

Booth

""

15:00-15:30

ClusterMakerRecipe

Allan

NatureProtocolsDemo

Piet

Booth

""

15:30-16:00

McodePluginRecipe

Chris

MiMiPpiDiscoveryRecipe(incl video)

Piet

Booth

evening

18:00-18:30

NatureProtocolsDemo

Piet

WikiPathwaysRecipe

Thomas

Booth

""

18:30-19:00

CommunityStructureLayoutRecipe

Allan (video)

DomainGraphRecipe, NetworkAnalyzerRecipe

Dorothea

Booth

""

19:00-19:30

NatureProtocolsDemo

Thomas (Piet)

AtheroSclerosisDemo

Allan

Booth

""

19:30-20:00

McodePluginRecipe

Chris

CyOogPowerGraphAnalysisRecipe

Matthias

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=%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

Hotel Opera

Annette, Allan

Friday 12:20 PM - UA 9362

Radisson SAS

Chris

Friday, noon-ish

Hotel Gothia Towers

InternationalConferenceOnSystemsBiologyDemos (last edited 2009-02-12 01:03:58 by localhost)

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