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~+'''Toronto - July 16th - 19th, 2008''' [http://cytoscape2008.eventbrite.com/ Registration Now Online] - '''Please help us plan by registering early!''' +~ ~+'''Toronto - July 16th - 19th, 2008''' [[http://cytoscape2008.eventbrite.com/|Registration Now Online]] - '''Please help us plan by registering early!''' +~
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[[TableOfContents()]] <<TableOfContents>>
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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. 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.
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 * [http://www.iscb.org/ismb2008/general_info.php ISMB] - July 19-23, 2008
 * [http://www.yeast-meet.org/ Yeast meeting] - July 22-27, 2008.
 * [[http://www.iscb.org/ismb2008/general_info.php|ISMB]] - July 19-23, 2008
 * [[http://www.yeast-meet.org/|Yeast meeting]] - July 22-27, 2008.
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If you have any comments or questions about the retreat, please send e-mail to [mailto:gary.bader@utoronto.ca Gary Bader]. If you have any comments or questions about the retreat, please send e-mail to [[mailto:gary.bader@utoronto.ca|Gary Bader]].
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|| 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)] || || {{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)]] ||
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||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) || ||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) ||
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||<rowbgcolor="#ffeecc">9am-5pm ||Technical brainstorm, software design session.[[BR]]Audience: Mainly Cytoscape software developers || ||<rowbgcolor="#ffeecc">9am-5pm ||Technical brainstorm, software design session.<<BR>>Audience: Mainly Cytoscape software developers ||
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||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 ||
||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]] ||
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||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]. || ||11:00am-11:30 ||Introduction to Spring Dynamic Modules - Kei Ono - Red Room. Some background reading on Spring + OSGi [[http://www.springframework.org/osgi|here]]. ||
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||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] || ||12:00pm-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]] ||
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||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. || ||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. ||
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||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 || ||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 ||
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||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''') ||
||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''') ||
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||<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 || ||<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 ||
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||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] ||
||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]] ||
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||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] ||
||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]] ||
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||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] ||
||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]] ||
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||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] ||
||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]] ||
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||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] ||
||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]] ||
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||7pm ||User community dinner at [http://www.brightpearlseafood.com/ Bright Pearl] Chinese Food Restaurant ('''Social event C''') || ||7pm ||User community dinner at [[http://www.brightpearlseafood.com/|Bright Pearl]] Chinese Food Restaurant ('''Social event C''') ||
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||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]] ||
||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>> ||
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||<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] ||
||<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]] ||
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||3:30pm-4:30pm ||[:CytoscapeRetreat2008/Brainstorm:Brainstorm and Discussion session] ||
||4:30pm-5:30pm ||[:CytoscapeRetreat2008/Book:Cytoscape book discussion] - Lead: Allan Kuchinsky, Agilent Technologies ||
||3:30pm-4:30pm ||[[CytoscapeRetreat2008/Brainstorm|Brainstorm and Discussion session]] ||
||4:30pm-5:30pm ||[[CytoscapeRetreat2008/Book|Cytoscape book discussion]] - Lead: Allan Kuchinsky, Agilent Technologies ||
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||7:30pm ||Social events: [:CytoscapeRetreat2008/NightOut:Night out in Toronto] ('''Social event E'''). Dinner on own. || ||7:30pm ||Social events: [[CytoscapeRetreat2008/NightOut|Night out in Toronto]] ('''Social event E'''). Dinner on own. ||
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||<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. ||
||<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. ||
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||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 ||
||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 ||
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||1:30pm-3:00pm ||[:CytoscapeRetreat2008/FeaturePrioritization:Cytoscape core feature prioritization, scheduling, work commitments] - Red Room || ||1:30pm-3:00pm ||[[CytoscapeRetreat2008/FeaturePrioritization|Cytoscape core feature prioritization, scheduling, work commitments]] - Red Room ||
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||3:45pm-5:00pm ||[:CytoscapeRetreat2008/BoardMeeting:Cytoscape Board Meeting] - Parallel session for board of director members - Black Room || ||3:45pm-5:00pm ||[[CytoscapeRetreat2008/BoardMeeting|Cytoscape Board Meeting]] - Parallel session for board of director members - Black Room ||
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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 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.
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 * [http://tdccbr.med.utoronto.ca Further information about the CCBR]  * [[http://tdccbr.med.utoronto.ca|Further information about the CCBR]]
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  * 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).   * 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).
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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. 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.
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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. 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.
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 * [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)
 * [[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)
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 * [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]
 * [[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]]

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:

  • 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:

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Unilever

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Agilent Laboratories

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Google Summer of Code

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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:

  • 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:

Some University of Toronto student residences:

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

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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