attachment:UnileverLogo.gif BR [http://www.unilever.com/ Unilever]

attachment:agilentlogo6.gif BR [http://www.agilent.com/labs/ Agilent Laboratories]

attachment:code_sm.png BR [http://code.google.com/soc/2008/ Google Summer of Code]

attachment:logo.gif BR [http://tdccbr.med.utoronto.ca/Home.aspx Terrence Donnelly Centre for Cellular and Molecular Biology (University of Toronto)]

TUESDAY July 15th

Arrival Day

Early arrivals welcome to visit the CCBR building to chat about Cytoscape. Visit room 602.

6:30pm

Social event in evening for early arrivals (Social event A) - At [http://www.thebedfordacademy.com/ Bedford Academy Pub] (near St. George Subway Station)

WEDNESDAY July 16th

CCBR Red Room, break out sessions in Black Room

8:30am

Light breakfast and coffee in Black Room

9am-5pm

Technical brainstorm, software design session.BRAudience: Mainly Cytoscape software developers

9:00am-9:10am

Welcome - Gary Bader - Red Room

9:10am-9:30am

Introduction to Cytoscape 3.0 - Mike Smoot - Red Room

9:30am-10:00am

Introduction to OSGi - Mike Smoot - Red Room Some background reading on OSGi: a [http://neilbartlett.name/blog/osgibook/ book] and some [http://neilbartlett.name/blog/osgi-articles/ examples].

10:00am-10:30am

Introduction to Spring - Kei Ono - Red Room. Some background reading on Spring: General [http://www.springframework.org/documentation documentation] and an [http://www.theserverside.com/tt/articles/article.tss?l=IntrotoSpring25 article].

10:30am-11am

Coffee break in Black Room

11:00am-11:30

Introduction to Spring Dynamic Modules - Kei Ono - Red Room. Some background reading on Spring + OSGi [http://www.springframework.org/osgi here].

11:30am-12:00pm

Bringing it all Together: Cytoscape 3.0, OSGi, and Spring - Mike Smoot - Red Room

12:00pm-12:30pm

Brief overview of the 3.0 [:Cytoscape 3.0/ModelDiscussions:Model Discussions and Resolutions] - Mike Smoot - Red Room. View the resulting API [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/model/network/package-summary.html here]

12:30pm-1:30pm

Lunch in Black Room

1:30pm - 3:00pm

The Cytoscape "View" bundles: [:Cytoscape 3.0/ViewModelDiscussions:ViewModel], [:Cytoscape 3.0/PresentationDiscussions:Presentation] and how they work with the Application Layer. Please read the linked discussions and see the [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/view/model/package-summary.html ViewModel] API for further information and don't forget to look at the [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/view/model/layout/package-summary.html layout] and [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/view/model/vizmap/package-summary.html vizmap] APIs as well.

3:00pm-3:30pm

Coffee Break - Black Room

3:30pm-5:00pm

The Cytoscape "Work" bundle: [:Cytoscape 3.0/CommandDiscussions:Command], [:Cytoscape 3.0/TunableDiscussion:Tunable], and [:Cytoscape 3.0/MonitorDiscussion:Monitor] - Mike Smoot - Red Room. Please read the discussions linked above and see the [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/command/package-summary.html command], [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/tunable/package-summary.html tunable], and [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/monitor/package-summary.html monitor] APIs for further details and explanation

5:00pm

Official end of Day 1

5:00pm-6:30pm

[:CytoscapeRetreat2008/Discussion:Continued discussions and break out sessions in CCBR at your leisure]

7pm

Dinner event at [http://www.messis.ca/main.html Messis European restaurant] (Social event B)

THURSDAY July 17th

CCBR Red Room

8:30am

Light breakfast and coffee outside Red Room

9am-5pm

Application showcase day.BRAudience: All Cytoscape users and developersBRDevelopers will showcase interesting new features they are building for CytoscapeBRUsers will present interesting new uses of Cytoscape

Schedule

9:00am-9:10am

Welcome in Red Room - Gary Bader

Visualization Session Chair: Gary Bader

9:10-9:40 - Scooter Morris, University of California, San Francisco, USA

[:CytoscapeRetreat2008/Scooter:Clusters and groups]

9:40-10:05 - Matthias Reimann, Biotechnology Center, Technische Universität Dresden, Germany

[:CytoscapeRetreat2008/Matthias:Power Graph Analysis with CyOog]

10:05-10:20 - Pekka Salmela, University of Turku, Finland

[:CytoscapeRetreat2008/Pekka:A multilevel graph layout plug-in for Cytoscape]

10:20-10:50 - Sarah Killcoyne, Institute for Systems Biology, Seattle, USA

[:CytoscapeRetreat2008/Sarah:Systems Biology Visualizations]

10:50am-11:20am

Coffee break outside Red Room

Google Summer of Code Session Chair: Alex Pico

11:20-11:35 - Maital Ashkenazi, Hebrew University of Jerusalem, Rehovot, Israel

[:CytoscapeRetreat2008/Maital:Cytoscape ESP: simple search of complex biological networks]

11:35-11:45 - Patrick McSweeney, Syracuse University, USA

[:CytoscapeRetreat2008/Patrick:Random Network Plugin]

11:45-11:55 - Victoria Mui, University of Toronto, Canada

[:CytoscapeRetreat2008/Victoria:Automatic label layout Plugin]

11:55-12:05 - Daniel Abel, Dept. of Biological Physics, ELTE, Hungary

[:CytoscapeRetreat2008/Daniel:Undirected edge support in cytoscape3]

12:05-12:15 - Steve Federowicz, University of California Santa Cruz, USA

[:CytoscapeRetreat2008/Steve:Boolean Mapping for Criteria Identification]

12:15-12:25 - Gang Su, Bioinformatics Program, University of Michigan, USA

[:CytoscapeRetreat2008/Gang:Normalizing Visualization with Hierarchical Community Structure]

12:30pm-1:30pm

Lunch. Pick up box lunch in Black Room.

Plugins Session Chair:

1:30-1:50 - Piet Molenaar, AMC Human Genetics, Amsterdam, The Netherlands

[:CytoscapeRetreat2008/Piet:R2 and Cytoscape: Graph based integration and analysis of molecular biological data]

1:50-2:00 - Vuk Pavlovic, University of Toronto, Canada

[:CytoscapeRetreat2008/Vuk:MCODE - Molecular Complex Detection plugin]

2:00-2:20 - Dorothea Emig, Max Planck Institute for Informatics, Saarbrücken, Germany

[:CytoscapeRetreat2008/Dorothea:DomainGraph: Integration of Expression Data with Interaction Networks]

2:20-2:35 - Jennifer Gardy, University of British Columbia, Vancouver, Canada

[:CytoscapeRetreat2008/Jennifer:Cerebral 2.0: A Cytoscape plugin for the network-based visualization of datasets from multiple experimental conditions]

2:35-2:45 - Laetitia Morrison, University of Toronto, Canada

[:CytoscapeRetreat2008/Laetitia:GOSlimmer: Creating custom GO Slim sets in Cytoscape]

3:00pm-3:30pm

Coffee break outside Red Room

Developers and Users Session Chair:

3:30-3:45 - Greg Wilson, University of Toronto, Canada

[:CytoscapeRetreat2008/Greg:DrProject]

3:45-4:00 - Barbara Mirel and Terry Weymouth, University of Michigan, USA

[:CytoscapeRetreat2008/Barbara:Support for Multi-Dimensional Information Through Perceptual Encoding: Next Steps]

Databases Session Chair: Allan Kuchinsky

4:00-4:15 - Jing Gao, University of Michigan, USA

[:CytoscapeRetreat2008/Jing:MiMI plugin]

4:15-4:30 - David States, University of Michigan, USA

[:CytoscapeRetreat2008/David:Michigan and NCIBI]

4:30-4:45 - Gary Bader, University of Toronto, Canada

[:CytoscapeRetreat2008/Gary:Pathway Commons plugin]

5:00pm

Official end of Day 1

5:00pm-6:30pm

Continued discussions in CCBR at your leisure

7pm

User community dinner at [http://www.brightpearlseafood.com/ Bright Pearl] Chinese Food Restaurant (Social event C)

FRIDAY July 18th

CCBR Red Room

8:30am

Light breakfast and coffee outside Red Room

9:00am-9:15am

Welcome in Red Room

9:15am-noon

[:CytoscapeRetreat2008/UserTutorial:User tutorial] (morning parallel session) Lead: Yeyejide Adeleye, UnileverBRRed RoomBRAudience: All Cytoscape usersBR

9:15am-noon

[:CytoscapeRetreat2008/DeveloperTutorial:Developer tutorial] (morning parallel session) Lead: Scooter Morris, UCSFBRBlack RoomBRAudience: All Cytoscape developersBR

10:30am-11am

Coffee break outside Red Room

Noon-1:30

Lunch, pick up in Black Room

1:30pm-5pm

User brainstorm and user meetingBRRed Room, break out sessions in Black RoomBRIdentify usability issues, request new features

1:30pm-3:00pm

[:CytoscapeRetreat2008/Brainstorm:Brainstorm session]

3:00pm-3:30pm

Coffee break outside Red Room

3:30pm-4:30pm

[:CytoscapeRetreat2008/Book:Cytoscape book discussion] - Lead: Allan Kuchinsky, Agilent Technologies

4:30pm-5:30pm

[:CytoscapeRetreat2008/Brainstorm:Brainstorm session]

6pm

Wine and cheese in 'Stone Lobby' of adjoining Medical Sciences Building (Social event D)

7:30pm

Social events: [:CytoscapeRetreat2008/NightOut:Night out in Toronto] (Social event E). Dinner on own.

SATURDAY July 19th

CCBR Red Room

8:30am

Light breakfast and coffee in Black Room

9am-5pm

Feature prioritization for Cytoscape 3.0BRAudience: Users and developers interested in Cytoscape developmentBRThis is a great chance to influence the development direction of Cytoscape.BRExpect lots of technical discussion.

9:00am-10:30am

The Cytoscape IO bundle: [:IODiscussions:IO Module discussions] - Mike Smoot - Red Room. Please read the linked discussion and look at the IO [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/io/read/package-summary.html Read] and [http://chianti.ucsd.edu/~mes/new_api/apidocs/org/cytoscape/io/write/package-summary.html Write] APIs for further information.

10:30am-11am

Coffee break in Black Room

10:30am-12:00am

[:CytoscapeRetreat2008/Design:Cytoscape design discussion: unresolved issues and summary] - Red Room

12:00pm-12:30pm

[:CytoscapeRetreat2008/FeaturePrioritization:Cytoscape core feature prioritization, scheduling, work commitments] - Red Room

12:30pm-1:30pm

Lunch in Black Room

1:30pm-3:00pm

[:CytoscapeRetreat2008/FeaturePrioritization:Cytoscape core feature prioritization, scheduling, work commitments] - Red Room

3:00pm-3:30pm

Coffee break in Black Room

3:30pm-3:45pm

Official wrap-up of retreat - Gary Bader - Red Room

3:45pm-5:00pm

[:CytoscapeRetreat2008/BoardMeeting:Cytoscape Board Meeting] - Parallel session for board of director members - Black Room

3:45pm-5:00pm

Continued discussions at leisure - Red Room

6pm

Dinner on own