Cytoscape Wiki
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
Contents
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:
ISMB - July 19-23, 2008
Yeast meeting - July 22-27, 2008.
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:
- Gary Bader
- Chris Workman
- Francis Ouellette
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:
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. |
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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. |
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. |
Schedule |
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9:00am-9:10am |
Welcome in Red Room - Gary Bader |
Visualization Session Chair: Gary Bader |
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9:10-9:40 - Scooter Morris, University of California, San Francisco, USA |
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9:40-10:05 - Matthias Reimann, Biotechnology Center, Technische Universität Dresden, Germany |
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10:05-10:20 - Pekka Salmela, University of Turku, Finland |
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10:20-10:50 - Sarah Killcoyne, Institute for Systems Biology, Seattle, USA |
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10:50am-11:20am |
Coffee break outside Red Room |
Google Summer of Code Session Chair: Alex Pico |
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11:20-11:35 - Maital Ashkenazi, Hebrew University of Jerusalem, Rehovot, Israel |
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11:35-11:45 - Patrick McSweeney, Syracuse University, USA |
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11:45-11:55 - Victoria Mui, University of Toronto, Canada |
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11:55-12:05 - Daniel Abel, Dept. of Biological Physics, ELTE, Hungary |
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12:05-12:15 - Steve Federowicz, University of California Santa Cruz, USA |
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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 |
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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 |
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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 |
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2:35-2:45 - Laetitia Morrison, University of Toronto, Canada |
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3:00pm-3:30pm |
Coffee break outside Red Room |
Developers and Users Session Chair: Allan Kuchinsky |
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3:30-3:45 - Greg Wilson, University of Toronto, Canada |
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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 |
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4:00-4:15 - Jing Gao, University of Michigan, USA |
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4:15-4:30 - David States, University of Michigan, USA |
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4:30-4:45 - Gary Bader, University of Toronto, Canada |
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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 |
9:15am-noon |
Developer tutorial (morning parallel session) Lead: Scooter Morris, UCSF |
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 |
1:30pm-3:00pm |
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3:00pm-3:30pm |
Coffee break outside Red Room |
3:30pm-4:30pm |
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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 |
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:
- 160 College St., Toronto, near the corner of University Ave and College St.
The Cytoscape retreat will be held in the following CCBR building conference rooms:
The Red Room (2nd floor) - Main location for Cytoscape retreat
The Black Room (2nd floor) - Break out room and food
Building security:
- The CCBR building requires a security card to access before 8am and after 6pm, and all day on weekends. Retreat representatives will be available to let people into the building on the weekend.
Registration FAQ
- Is there a poster session?
A poster session is not currently planned, however, if you're interested, email Gary ( gary.bader@utoronto.ca ). If there is enough interest, we can organize a session.
- How do I sign up for the application showcase day?
- During the registration process, please answer the question: "If you would like to present your work in the application showcase day (Thursday July 17th), please enter your presentation title and a brief summary of what you will present. The organizers will contact you for further information."
- Is there a discounted hotel rate?
Yes. We've negotiated a special rate at the Delta Chelsea hotel for the Cytoscape retreat. To reserve, call the hotel and let them know you are with "University of Toronto". You must reserve a room by July 3rd to get this rate. The rate is $130 Canadian/night (+ tax) for single/double and $150 for triple. Please reserve early, as rooms are being booked quickly. If you've already reserved a room, you can call the hotel to re-reserve using this discounted rate. http://www.deltahotels.com/hotels/hotels.php?hotelId=10
- Will there be internet access at the retreat?
- Yes, wireless internet access will be provided. Contact us if you need wired access. Power bars and extension cords for laptops will also be available.
- Are there any other interesting events that are going on around the same time as the Cytoscape retreat?
Of course there is ISMB, its satellite meetings, the yeast meeting. There is also Software DemoCamp. If you're interested in going to this, please contact Greg Wilson for more information. There is also CAST 2008 - The 3rd Annual Conference of the Association for Software Testing (CAST).
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:
Delta Chelsea Hotel Large hotel
Baldwin Village Inn Bed and Breakfast (limited number of rooms)
Beverley Place Bed and Breakfast (limited number of rooms)
Some University of Toronto student residences: