= Cytoscape Developer Retreat 2008 =
~+'''Toronto - July 16th - 19th, 2008''' [[http://cytoscape2008.eventbrite.com/|Registration Now Online]] - '''Please help us plan by registering early!''' +~

'''Theme for 2008: Developer and user community outreach'''

<<TableOfContents>>

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, [[http://www.iscb.org/ismb2008/general_info.php|Intelligent Systems for Molecular Biology (ISMB)]], and the [[http://www.yeast-meet.org/|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:

 * [[http://www.iscb.org/ismb2008/general_info.php|ISMB]] - July 19-23, 2008
 * [[http://www.yeast-meet.org/|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 [[mailto:gary.bader@utoronto.ca|Gary Bader]].

The 2008 Cytoscape retreat is generously sponsored by:
|| {{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)]] ||


= 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.
||<rowbgcolor="#ffeeaa">'''TUESDAY July 15th''' ||Arrival Day ||
||||<style="TEXT-ALIGN: center">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) ||
||<rowbgcolor="#ffeeaa">'''WEDNESDAY July 16th''' ||CCBR Red Room, break out sessions in Black Room ||
||8:30am ||Light breakfast and coffee in Black Room ||
||<rowbgcolor="#ffeecc">9am-5pm ||Technical brainstorm, software design session.<<BR>>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 [[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]]. [[attachment: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 [[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''') ||


== 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.
||<rowbgcolor="#ffeeaa">'''THURSDAY July 17th''' ||CCBR Red Room ||
||8:30am ||Light breakfast and coffee outside Red Room ||
||<rowbgcolor="#ffeecc">9am-5pm ||Application showcase day.<<BR>>Audience: All Cytoscape users and developers<<BR>>Developers will showcase interesting new features they are building for Cytoscape<<BR>>Users will present interesting new uses of Cytoscape ||
||||<style="TEXT-ALIGN: center">'''Schedule''' ||
||9:00am-9:10am ||Welcome in Red Room - Gary Bader ||
||||<style="TEXT-ALIGN: center">'''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 ||
||||<style="TEXT-ALIGN: center">'''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. ||
||||<style="TEXT-ALIGN: center">'''Plugins''' Session Chair: Piet Molenaar ||
||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 ||
||||<style="TEXT-ALIGN: center">'''Developers and Users''' Session Chair: Allan Kuchinsky ||
||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]] ||
||||<style="TEXT-ALIGN: center">'''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''') ||
||<rowbgcolor="#ffeeaa">'''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, Unilever<<BR>>Red Room<<BR>>Audience: All Cytoscape users<<BR>> ||
||9:15am-noon ||[[CytoscapeRetreat2008/DeveloperTutorial|Developer tutorial]] (morning parallel session) Lead: Scooter Morris, UCSF<<BR>>Black Room<<BR>>Audience: All Cytoscape developers<<BR>> ||
||10:30am-11am ||Coffee break outside Red Room ||
||Noon-1:30 ||Lunch, pick up in Black Room ||
||<rowbgcolor="#ffeecc">1:30pm-4:30pm ||User brainstorm and user meeting<<BR>>Red Room, break out sessions in Black Room<<BR>>Identify usability issues, request new features ||
||1:30pm-3:00pm ||[[CytoscapeRetreat2008/Brainstorm|Brainstorm and Discussion session]] ||
||3:00pm-3:30pm ||Coffee break outside Red Room ||
||3:30pm-4:30pm ||[[CytoscapeRetreat2008/Brainstorm|Brainstorm and Discussion session]] ||
||4:30pm-5:30pm ||[[CytoscapeRetreat2008/Book|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: [[CytoscapeRetreat2008/NightOut|Night out in Toronto]] ('''Social event E'''). Dinner on own. ||
||<rowbgcolor="#ffeeaa">'''SATURDAY July 19th''' ||CCBR Red Room ||
||8:30am ||Light breakfast and coffee in Black Room ||
||<rowbgcolor="#ffeecc">9am-5pm ||Feature prioritization for Cytoscape 3.0<<BR>>Audience: Users and developers interested in Cytoscape development<<BR>>This is a great chance to influence the development direction of Cytoscape.<<BR>>Expect 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 ||


= Location =
The Cytoscape retreat will be held at the [[http://rrs.osm.utoronto.ca/map/f?p=110:4:9399106623511446478::::P4_BLDG_KEY:160|Donnelly Centre for Cellular and Biomolecular Research (CCBR)]], which can be seen at the lower right side of the [[http://rrs.osm.utoronto.ca/map/|University of Toronto campus map]] or on [[http://maps.google.com/maps/ms?f=q&hl=en&geocode=&ie=UTF8&msa=0&msid=114604530129432068866.000451aebfc36e9770cbb&ll=43.662035,-79.393387&spn=0.036852,0.037637&z=15|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.
 * [[http://tdccbr.med.utoronto.ca|Further information about the CCBR]]
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 [[http://barcamp.org/DemoCampToronto18|Software DemoCamp]]. If you're interested in going to this, please contact [[http://www.cs.utoronto.ca/~gvwilson/|Greg Wilson]] for more information. There is also [[http://www.associationforsoftwaretesting.org/drupal/cast2008|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 [[http://www.flyporter.com/|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 [[http://www.iscb.org/ismb2008/general_info.php|ISMB 2008]] or [[http://www.yeast-meet.org/|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:

 * [[http://www.deltahotels.com/hotels/hotels.php?hotelId=10|Delta Chelsea Hotel]] Large hotel
 * [[http://www.baldwininn.com/|Baldwin Village Inn]] Bed and Breakfast (limited number of rooms)
 * [[http://www.bbcanada.com/504.html?showpage=1|Beverley Place]] Bed and Breakfast (limited number of rooms)
Some University of Toronto student residences:

 * [[http://www.trinity.utoronto.ca/Summer_Residence/default.htm|New College Residence (anyone)]]
 * [[http://www.trinity.utoronto.ca/Summer_Residence/default.htm|Trinity College (students only)]]
 * [[http://www.uc.utoronto.ca/content/view/125/795/|University College (students only)]]
 * [[http://www.vicu.utoronto.ca/facilities/accommodations.htm|Victoria College (anyone)]]
 * [[http://wdw.utoronto.ca/residence/index.php/home/indexx/C78/prospective|Woodsworth College (conference groups/anyone?)]]
 * [[http://www.utoronto.ca/massey/summer.html|Massey College]]