Cytoscape Wiki
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
- 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 |
Annotate network |
Overlay Gene Expression Data on Network |
jActiveModules? |
Everyone |
Everyone |
||
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 |
|
Find possible complexes, protein families, functional relationships and view in biological context |
Allan |
?? |
|
||
7 |
|
1. explore functional relationships 2. get sequence similarities that are otherwise hidden by low scoring from homology networks |
Matthias |
?? |
|
||
8 |
|
find community structures in large biological networks, which may infer protein complexes and biological pathways. |
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 |
|
|
|
Scooter |
draft |
|
|
draft |
|
|
|
Scooter |
draft |
|
|
draft |
|
|
|
Gary |
done |
|
|
|
|
|
|
David, Jing |
done |
|
|
draft |
from David States, at http://www.youtube.com/watch?v=R5yFOiRb18I&feature=related |
|
|
AllanK |
see comments |
|
|
see comments |
|
what is in the actual paper will suffice. Use retreat2008_tutorial.doc |
|
Thomas |
done |
|
|
done |
|
|
|
Matthias |
done |
done |
done |
done |
|
|
|
Dorothea |
done |
|
|
done |
|
|
|
Mario |
done |
|
|
done |
|
|
|
Gang |
done |
|
|
|
|
||
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 |
Allan |
Piet |
Booth |
||
"" |
13:30-14:00 |
Thomas |
Piet |
Booth |
||
"" |
14:00-14:30 |
Dorothea |
Allan |
Booth |
||
"" |
14:30-15:00 |
Matthias |
Allan (video?) |
Allan and/or Piet assist |
||
"" |
15:00-15:30 |
Allan |
Piet |
Booth |
||
"" |
15:30-16:00 |
Chris |
MiMiPpiDiscoveryRecipe(incl video) |
Piet |
Booth |
|
evening |
18:00-18:30 |
Piet |
Thomas |
Booth |
||
"" |
18:30-19:00 |
Allan (video) |
Dorothea |
Booth |
||
"" |
19:00-19:30 |
Thomas (Piet) |
Allan |
Booth |
||
"" |
19:30-20:00 |
Chris |
Matthias |
Booth |
||
Mon Aug 25th afternoon |
13:00-13:30 |
Allan |
Piet |
Booth |
||
"" |
13:30-14:00 |
Thomas |
Piet |
Booth |
||
"" |
14:00-14:30 |
Dorothea |
Allan |
Booth |
||
"" |
14:30-15:00 |
Matthias |
Allan (video?) |
Allan and/or Piet assist |
||
"" |
15:00-15:30 |
Allan |
Piet |
Booth |
||
"" |
15:30-16:00 |
Chris |
MiMiPpiDiscoveryRecipe(incl video) |
Piet |
Booth |
|
Tue Aug 26th afternoon |
13:00-13:30 |
Allan |
Piet |
Booth |
||
"" |
13:30-14:00 |
Thomas |
Piet |
Booth |
||
"" |
14:00-14:30 |
Dorothea |
Allan |
Booth |
||
"" |
14:30-15:00 |
Matthias |
Allan (video?) |
Booth |
||
"" |
15:00-15:30 |
Allan |
Piet |
Booth |
||
"" |
15:30-16:00 |
Chris |
MiMiPpiDiscoveryRecipe(incl video) |
Piet |
Booth |
|
evening |
18:00-18:30 |
Piet |
Thomas |
Booth |
||
"" |
18:30-19:00 |
Allan (video) |
Dorothea |
Booth |
||
"" |
19:00-19:30 |
Thomas (Piet) |
Allan |
Booth |
||
"" |
19:30-20:00 |
Chris |
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 |
|
Annette, Allan |
Friday 12:20 PM - UA 9362 |
|
Chris |
Friday, noon-ish |