Cytoscape Developer Retreat 2008

Toronto - July 16th - 19th, 2008 Registration Now Online - Please help us plan by registering early!

Theme for 2008: Developer and user community outreach

On 16th – 19th July 2008 we will be hosting the 6th Annual Cytoscape Retreat at the Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada.

This year’s meeting is particularly exciting since it is the first time it will be held in Canada and will be purely user and developer community focused. It is also close to the major international computational biology conference, Intelligent Systems for Molecular Biology (ISMB), and the International Yeast Meeting, to be held in Toronto in July. We expect close to 100 participants interested in biological pathway and network analysis. Social activities around the meeting are also scheduled.

Related conference schedules:

Cytoscape is jointly developed by the groups of Benno Schwikowski (Pasteur Institute, Paris), Trey Ideker (University of California San Diego), Chris Sander (Memorial Sloan-Kettering Cancer Center), Lee Hood (Institute for Systems Biology, Seattle), Annette Adler (Agilent Technologies, Santa Clara), Gary Bader (University of Toronto) and Bruce Conklin (Gladstone Institute UCSF, GenMAPP). Funding for Cytoscape is provided by the U.S. National Institute of General Medical Sciences of the National Institutes of Health under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC. These groups are dedicated to maintaining and developing Cytoscape and providing support to the user community.

The organization committee this year is:

If you have any comments or questions about the retreat, please send e-mail to Gary Bader.

The 2008 Cytoscape retreat is generously sponsored by:

UnileverLogo.gif
Unilever

agilentlogo6.gif
Agilent Laboratories

code_sm.png
Google Summer of Code

logo.gif
Terrence Donnelly Centre for Cellular and Molecular Biology (University of Toronto)

Schedule

Technical session

The technical session will mainly be informal and technically focused with all major Cytoscape team members gathered together to set new directions for Cytoscape, plan new features and collaboratively work on designing code.

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 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.
Audience: 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 book and some examples.

10:00am-10:30am

Introduction to Spring - Kei Ono - Red Room. Some background reading on Spring: General documentation and an article. spring-osgi.pdf

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 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 Model Discussions and Resolutions - Mike Smoot - Red Room. View the resulting API here

12:30pm-1:30pm

Lunch in Black Room

1:30pm - 3:00pm

The Cytoscape "View" bundles: ViewModel, Presentation and how they work with the Application Layer. Please read the linked discussions and see the ViewModel API for further information and don't forget to look at the layout and vizmap APIs as well.

3:00pm-3:30pm

Coffee Break - Black Room

3:30pm-5:00pm

The Cytoscape "Work" bundle: Command, Tunable, and Monitor - Mike Smoot - Red Room. Please read the discussions linked above and see the command, tunable, and monitor APIs for further details and explanation

5:00pm

Official end of Day 1

5:00pm-6:30pm

Continued discussions and break out sessions in CCBR at your leisure

7pm

Dinner event at Messis European restaurant (Social event B)

User session

The user session is geared towards all users of Cytoscape, including researchers and plugin developers. These sessions will showcase work users are doing with Cytoscape, provide tutorial opportunities and provide a forum for user feedback on Cytoscape features, bugs and development plans.

THURSDAY July 17th

CCBR Red Room

8:30am

Light breakfast and coffee outside Red Room

9am-5pm

Application showcase day.
Audience: All Cytoscape users and developers
Developers will showcase interesting new features they are building for Cytoscape
Users 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

Clusters and groups

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

Power Graph Analysis with CyOog

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

A multilevel graph layout plug-in for Cytoscape

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

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

Cytoscape ESP: simple search of complex biological networks

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

Random Network Plugin

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

Automatic label layout Plugin

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

Undirected edge support in cytoscape3

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

Boolean Mapping for Criteria Identification

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

Normalizing Visualization with Hierarchical Community Structure

12:30pm-1:30pm

Lunch. Pick up box lunch in Black Room.

Plugins Session Chair: Piet Molenaar

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

R2 and Cytoscape: Graph based integration and analysis of molecular biological data

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

MCODE - Molecular Complex Detection plugin

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

DomainGraph: Integration of Expression Data with Interaction Networks

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

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

GOSlimmer: Creating custom GO Slim sets in Cytoscape

3:00pm-3:30pm

Coffee break outside Red Room

Developers and Users Session Chair: Allan Kuchinsky

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

DrProject

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

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

MiMI plugin

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

Michigan and NCIBI

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

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 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

User tutorial (morning parallel session) Lead: Yeyejide Adeleye, Unilever
Red Room
Audience: All Cytoscape users

9:15am-noon

Developer tutorial (morning parallel session) Lead: Scooter Morris, UCSF
Black Room
Audience: All Cytoscape developers

10:30am-11am

Coffee break outside Red Room

Noon-1:30

Lunch, pick up in Black Room

1:30pm-4:30pm

User brainstorm and user meeting
Red Room, break out sessions in Black Room
Identify usability issues, request new features

1:30pm-3:00pm

Brainstorm and Discussion session

3:00pm-3:30pm

Coffee break outside Red Room

3:30pm-4:30pm

Brainstorm and Discussion session

4:30pm-5:30pm

Cytoscape book discussion - Lead: Allan Kuchinsky, Agilent Technologies

6pm

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

7:30pm

Social events: 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 3.0
Audience: Users and developers interested in Cytoscape development
This is a great chance to influence the development direction of Cytoscape.
Expect lots of technical discussion.

9:00am-10:30am

The Cytoscape IO bundle: IO Module discussions - Mike Smoot - Red Room. Please read the linked discussion and look at the IO Read and Write APIs for further information.

10:30am-11am

Coffee break in Black Room

10:30am-12:00am

Cytoscape design discussion: unresolved issues and summary - Red Room

12:00pm-12:30pm

Cytoscape core feature prioritization, scheduling, work commitments - Red Room

12:30pm-1:30pm

Lunch in Black Room

1:30pm-3:00pm

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

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

Location

The Cytoscape retreat will be held at the Donnelly Centre for Cellular and Biomolecular Research (CCBR), which can be seen at the lower right side of the University of Toronto campus map or on Google Maps. Note: all venues, including hotel and restaurants, are marked on the Google Map.

The address is:

The Cytoscape retreat will be held in the following CCBR building conference rooms:

Building security:

Registration FAQ

Travel and Accommodation

We recommend Toronto International Airport (YYZ) or if you live in Canada or the US, Toronto City Centre Airport (YTZ) serviced by Porter Airlines. They are both provide easy access to the city, with numerous shuttles, taxis, car services and public transportation options.

July is a big conference month in Toronto. We highly recommend making your hotel reservations ASAP! Try hotels.com or check out the options listed at the ISMB 2008 or International Yeast Meeting 2008 conference websites. These conferences are happening just after the Cytoscape retreat at nearby city locations.

Some nearby recommended Bed and Breakfasts and Hotels are:

Some University of Toronto student residences:

CytoscapeRetreat2008 (last edited 2009-02-12 01:03:17 by localhost)

MoinMoin Appliance - Powered by TurnKey Linux