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Cytoscape Developer Retreat 2010

July 18th-20th, 2010 - ONLINE REGISTRATION CLOSED - For late registration E-mail Jacki Troy(jtroy@umich.edu)

University of Michigan, North Campus Research Complex - 2800 Plymouth Road, Ann Arbor, Michigan

Contents

Cytoscape Developer Retreat 2010
Schedule
Speakers
Location & Info
Travel and Accommodation
1. Air Travel
2. Hotels
FAQ

On July 18th-20th, 2010, we will be hosting the 7th annual Cytoscape Retreat and Symposium at the North Campus Research Complex, University of Michigan, Ann Arbor, Michigan.

This year we are excited to have the meeting in Ann Arbor, and this will be the first major scientific meeting held at the newly opened North Campus Research Complex, a former Pfizer site, now being expanded as a state of the art research facility for U-M collaborations. The meeting will also feature a day long symposium on "Networks in Disease and Health", with several featured speakers including Dr. Leroy Hood, and Dr. Stephen Friend.

The meeting is jointly hosted by the The Center for Computational Medicine and Bioinformatics and the The National Center for Integrative Biomedical Informatics, and is sponsored and supported by the Cytoscape Consortium and Agilent Laboratories.

If you would like to submit an abstract to present a demo or have any questions about the retreat E-mail Jacki Troy (jtroy@umich.edu)

Download Cytoscape Retreat Flyer

Schedule

Sunday, July 18, 2010

Developer Tutorial (Samad Lotia, Agilent) Download PDF or LaTeX source (requires beamer and pdfLaTeX)	10:00am - 12:00noon
User Tutorial (Scooter Morris, UCSF) Download PDF or Powerpoint	10:00am - 12:00noon
LUNCH	12:00 - 01:30pm
Plugin Demonstrations	01:30pm - 05:30pm
Giovanni Scardoni - Analyzing biological networks with CentiScaPe Watch Video
Sasha Tkachev - Web Service Client and Server for PhosphoSitePlus database Watch Video
Kozo Nishida - Importing KEGG pathway and mapping custom node graphics on Cytoscape (Project Web Site) Watch Video
Morgan Taschuk - CID: Exploring Interactomes with Cytoscape Watch Video
Terry Weymouth - Metscape Plugin for Visualization and Analysis of Genes and Metabolites Watch Video
Gregory Hannum - A Cytoscape plugin for Physical and Genetic Interaction Alignment – PanGIA Watch Video
James Vlasblom - Ortho-Nets: Simultaneous analysis and visualization of protein-interaction network environments of orthologous genes in different organisms Watch Video
Jochen Weile - Concise visualizations of integrated datasets with the OndexView Cytoscape plug-in Watch Video
Jason Montojo - GeneMANIA Cytoscape Plugin: Fast desktop gene function prediction Watch Video
Ruth Isserlin - Enrichment Map: A Cytoscape Plugin to enable visualization and interpretation of Gene-Set Enrichment Analysis Watch Video
Terry Weymouth - The Cytoscape MiMI Plugin with the NCIBI/MiMI Attribute Browser Watch Video
Gang Su - Cytoscape plug-ins: GLay v.2 and GSearcher Watch Video
Developer Dinner	06:00pm

Monday, July 19, 2010

Networks in Disease and Health Symposium Day

Registration and Continental Breakfast (Building 18 Lobby and Cafeteria)	08:00am - 08:30am
Brian Athey, Ph.D. / Gil Omenn, MD, Ph.D. - Welcome Watch Video	08:30am - 08:45am
Lee Hood, M.D., Ph.D. - P4 Medicine: Catalyzing a Revolution from Reactive to Proactive Medicine Watch Video	08:45am - 09:30am
Charlie Boone, Ph.D. - The Genetic Landscape of a Cell Watch Video	09:30am - 10:15am
BREAK	10:15am - 10:25am
Mark Newman, Ph.D. - Social Networks and the Spread of Infectious Disease Watch Video	10:30am - 11:15am
Eric Neuman, Ph.D. - Visual Analysis of the Web of Linked Data: the SQL Plugin for Cytoscape* Watch Video	11:15am - 12:00pm
LUNCH	12:00pm - 01:00pm
Edward Rietman, Ph.D. - Observation of spatial protein-protein interactome dynamics in Arabidopsis root Watch Video	01:00pm - 01:45pm
Peter Zandstra, Ph.D. - Watch Video	01:45pm - 02:30pm
BREAK	02:30pm - 02:40pm
Brian Athey, Ph.D. - CTSA Biomedical Informatics as a Means to Leverage Local and National Resources to Improve Clinical Research and Translational Effectiveness Watch Video	03:30pm - 04:00pm
Stephen Friend, M.D., Ph.D. - Better Maps of Disease, Not Just What But How, Building a Commons For Evolving Generative Models of Disease Watch Video	04:00pm - 05:00pm
Poster Session & Reception	05:00pm - 06:30pm
Developer Dinner	06:30pm
Board of Director's Dinner	06:30pm

Tuesday, July 20, 2010

Continental Breakfast	08:30am - 09:00am
Developer Working Sessions "Hack-A-Thon" (B10 Large Conference Room A&B)	09:00am - 12:00pm
LUNCH	12:00pm - 01:30pm
Developer Working Sessions "Hack-A-Thon" (B10 Large Conference Room A&B)	01:30pm - 04:00pm

/HackathonSchedule

Speakers

Dr. Leroy Hood, M.D., Ph.D.

Founder and President

Institute for Systems Biology

Seattle, Washington

Dr. Stephen H. Friend, M.D., Ph.D.

Co-founder, President, and Chief Executive Officer

Sage Bionetworks

Dr. Charlie Boone, Ph.D.

Professor, Department of Medical Research

Canada Research Chair Banting and Best

University of Toronto

Dr. Mark Newman, Ph.D.

Paul Dirac Collegiate Professor of Physics

Professor, Center for the Study of Complex Systems

University of Michigan

Dr. Peter Zandstra, Ph.D.

Professor, Canada Research Chair in Stem Cell Bioengineering

University of Toronto

Dr. Gil Omenn

Professor of Internal Medicine, Human Genetics, and Public Health

Director, Center for Computational Medicine and Bioinformatics

Location & Info

The Cytoscape retreat will be held at the University of Michigan, North Campus Research Complex in Ann Arbor, Michigan. Google Map

For Ann Arbor visitor information, including finding a place to eat or something to do, visit: http://www.visitannarbor.org/

Travel and Accommodation

Air Travel

We recommend the Detroit Metro Airport (DTW) if you are flying in.

For transport to and from the airport see: Custom Transit or Metro Cars

Hotels

Some nearby recommended Hotels are:

Hampton Inn - $92.00/night (Group code: CYT)

Cytoscape reservation group rate link - Hampton Inn

2300 Green Road, Ann Arbor, MI 48105

Phone - 734-996-4444

Holiday Inn - $92.00/night

Cytoscape reservation group rate link - Holiday Inn

3600 Green Road, Ann Arbor, MI 48105

Phone - 734-769-9800

FAQ

Is there a poster session?

Yes, there will be a poster sessions and reception from 5pm-6:30pm on Monday, July 19th.

How do I sign up for the poster session?

If you would like to submit an abstract for the poster session e-mail Jacki Troy (jtroy@umich.edu).

How do I sign up for the plugin demo?

If you would like to submit an abstract for the plugin demonstration e-mail Jacki Troy (jtroy@umich.edu).

Will there be internet access at the retreat?

Yes, there will be free wireless access for all attendees.

Is there a discounted hotel rate?

Yes, we have negotiated group rates at both the Holiday Inn and Hampton Inn listed above.

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-=== July 18th-20th, 2010 ===

=== U-M North Campus Research Complex - 2800 Plymouth Road, Ann Arbor, Michigan ===
+'''July 18th-20th, 2010 - ONLINE REGISTRATION CLOSED''' - For late registration E-mail Jacki Troy(jtroy@umich.edu)
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+Line 4:
-On July 18th-20th, 2010 we will be hosting the 7th Annual Cytoscape Retreat at the North Campus Research Complex, University of Michigan, Ann Arbor.
+'''University of Michigan, North Campus Research Complex - 2800 Plymouth Road, Ann Arbor, Michigan'''
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-Details, including registration information and full schedule, coming soon ...
+<<TableOfContents>>
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-If you would like to submit an abstract to present a demo or have any questions about the Cytoscape Retreat E-mail Jacki Troy (jtroy@umich.edu)
+On July 18th-20th, 2010, we will be hosting the 7th annual Cytoscape Retreat and Symposium at the North Campus Research Complex,  University of Michigan, Ann Arbor, Michigan.



This year we are excited to have the meeting in Ann Arbor,  and this will be the first major scientific meeting held at the newly opened North Campus Research Complex, a former Pfizer site, now being expanded as a state of the art research facility for U-M collaborations.  The meeting will also feature a day long symposium on "Networks in Disease and Health", with several featured speakers including Dr. Leroy Hood, and Dr. Stephen Friend.  



The meeting is jointly hosted by the [[http://ccmb.med.umich.edu | The Center for Computational Medicine and Bioinformatics]] and the [[http://www.ncibi.org | The National Center for Integrative Biomedical Informatics]], and is sponsored and supported by the [[http://cytoscape.org/|Cytoscape Consortium]] and [[http://www.agilent.com/labs/|Agilent Laboratories]]. 



'''If you would like to submit an abstract to present a demo or have any questions about the retreat E-mail Jacki Troy (jtroy@umich.edu)'''
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+Line 18:
-== Tentative Schedule ==
+== Schedule ==
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+Line 20:
-|| Developer Session || 10:00am - 12:00noon ||

|| User Session || 10:00am - 12:00noon ||

|| Lunch || 12:00 - 1:30pm ||

|| Plugin Demonstrations || 1:30pm - 5:30pm ||

|| Developer Dinner || 6:00pm ||
+|| Developer Tutorial (Samad Lotia, Agilent) Download [[http://cytoscape.wodaklab.org/wiki/CytoscapeRetreat2010?action=AttachFile&do=get&target=CytoscapeDevelopersTutorial.pdf|PDF]] or [[http://cytoscape.wodaklab.org/wiki/CytoscapeRetreat2010?action=AttachFile&do=get&target=CytoscapeDevelopersTutorial.tar|LaTeX source]] (requires beamer and pdfLaTeX)|| 10:00am - 12:00noon ||

|| User Tutorial (Scooter Morris, UCSF) Download [[http://cytoscape.wodaklab.org/wiki/CytoscapeRetreat2010?action=AttachFile&do=get&target=CytoscapeUsersTutorial.pdf|PDF]] or [[http://cytoscape.wodaklab.org/wiki/CytoscapeRetreat2010?action=AttachFile&do=get&target=CytoscapeUsersTutorial.ppt|Powerpoint]]|| 10:00am - 12:00noon ||

|| '''LUNCH''' || 12:00 - 01:30pm ||

|| '''Plugin Demonstrations''' || 01:30pm - 05:30pm ||

|| Giovanni Scardoni - ''Analyzing biological networks with CentiScaPe'' [[https://connect.umms.med.umich.edu/p46592388/|Watch Video]]|| ||

|| Sasha Tkachev - ''Web Service Client and Server for PhosphoSitePlus database'' [[https://connect.umms.med.umich.edu/p27229451/|Watch Video]] || ||

|| Kozo Nishida - ''Importing KEGG pathway and mapping custom node graphics on Cytoscape'' ([[http://code.google.com/p/kgmlreader/|Project Web Site]]) [[https://connect.umms.med.umich.edu/p40471776/|Watch Video]] || ||

|| Morgan Taschuk - ''CID: Exploring Interactomes with Cytoscape'' [[https://connect.umms.med.umich.edu/p40471776/|Watch Video]] || ||

|| Terry Weymouth - ''Metscape Plugin for Visualization and Analysis of Genes and Metabolites'' [[https://connect.umms.med.umich.edu/p39741703/|Watch Video]] || ||

|| Gregory Hannum - ''A Cytoscape plugin for Physical and Genetic Interaction Alignment – PanGIA'' [[https://connect.umms.med.umich.edu/p49062635/|Watch Video]] || ||

|| James Vlasblom - ''Ortho-Nets: Simultaneous analysis and visualization of protein-interaction network environments of orthologous genes in different organisms'' [[https://connect.umms.med.umich.edu/p58383567/|Watch Video]] || ||

|| Jochen Weile - ''Concise visualizations of integrated datasets with the OndexView Cytoscape plug-in'' [[https://connect.umms.med.umich.edu/p67704499/|Watch Video]]|| ||

|| Jason Montojo - ''GeneMANIA Cytoscape Plugin: Fast desktop gene function prediction'' [[https://connect.umms.med.umich.edu/p81685897/|Watch Video]] || ||

|| Ruth Isserlin - ''Enrichment Map: A Cytoscape Plugin to enable visualization and interpretation of Gene-Set Enrichment Analysis'' [[https://connect.umms.med.umich.edu/p91006829/|Watch Video]] || ||

|| Terry Weymouth - ''The Cytoscape MiMI Plugin with the NCIBI/MiMI Attribute Browser'' [[https://connect.umms.med.umich.edu/p24309159/|Watch Video]]|| ||

|| Gang Su - ''Cytoscape plug-ins: GLay v.2 and GSearcher'' [[https://connect.umms.med.umich.edu/p33621091/|Watch Video]] || ||

|| '''Developer Dinner''' || 06:00pm ||
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+Line 39:
-|| Registration and Continental Breakfast || 8:00am - 9:00am ||

|| Kick Off - Dr. Ora Pescovitz || 8:30am - 9:00am ||

|| Symposium presentations by invited speakers || Final speakers and times TBA ||

|| Poster Session & Reception || 5:00pm - 6:30pm ||

|| Developer Dinner || 6:30pm ||
+'''Networks in Disease and Health Symposium Day'''

|| '''Registration and Continental Breakfast (Building 18 Lobby and Cafeteria)''' || 08:00am - 08:30am ||

|| Brian Athey, Ph.D. / Gil Omenn, MD, Ph.D. - ''Welcome'' [[https://connect.umms.med.umich.edu/p24139142/|Watch Video]] || 08:30am - 08:45am ||

|| Lee Hood, M.D., Ph.D. - ''P4 Medicine: Catalyzing a Revolution from Reactive to Proactive Medicine '' [[https://connect.umms.med.umich.edu/p99427671/|Watch Video]]|| 08:45am - 09:30am ||

|| Charlie Boone, Ph.D. - ''The Genetic Landscape of a Cell'' [[https://connect.umms.med.umich.edu/p46702399/|Watch Video]]|| 09:30am - 10:15am ||

|| '''BREAK''' || 10:15am - 10:25am ||

|| Mark Newman, Ph.D. - ''Social Networks and the Spread of Infectious Disease'' [[https://connect.umms.med.umich.edu/p69274656/|Watch Video]] || 10:30am - 11:15am ||

|| Eric Neuman, Ph.D. - ''Visual Analysis of the Web of Linked Data: the S*QL Plugin for Cytoscape'' [[https://connect.umms.med.umich.edu/p79605689/|Watch Video]] || 11:15am - 12:00pm ||

|| '''LUNCH''' || 12:00pm - 01:00pm ||

|| Edward Rietman, Ph.D. - ''Observation of spatial protein-protein interactome dynamics in Arabidopsis root '' [[https://connect.umms.med.umich.edu/p43782107/|Watch Video]] || 01:00pm - 01:45pm ||

|| Peter Zandstra, Ph.D. - [[https://connect.umms.med.umich.edu/p58773606/|Watch Video]] || 01:45pm - 02:30pm ||

|| '''BREAK''' || 02:30pm - 02:40pm ||

|| Brian Athey, Ph.D. - ''CTSA Biomedical Informatics as a Means to Leverage Local and National Resources to Improve Clinical Research and Translational Effectiveness'' [[https://connect.umms.med.umich.edu/p91396868/|Watch Video]]|| 03:30pm - 04:00pm ||

|| Stephen Friend, M.D., Ph.D. - ''Better Maps of Disease, Not Just What But How, Building a Commons For Evolving Generative Models of Disease'' [[https://connect.umms.med.umich.edu/p71294858/|Watch Video]] || 04:00pm - 05:00pm ||

|| '''Poster Session & Reception''' || 05:00pm - 06:30pm ||

|| '''Developer Dinner''' || 06:30pm ||

|| '''Board of Director's Dinner''' || 06:30pm ||
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-|| Continental Breakfast || 8:30am ||

|| Developer Working Sessions "Hack-A-Thon" || 9:00am - 12:00noon ||

|| Lunch || 12:00 - 1:30pm ||

|| Developer Working Sessions "Hack-A-Thon" || 1:30pm - 4:00pm ||
+|| '''Continental Breakfast''' || 08:30am - 09:00am||

|| Developer Working Sessions "Hack-A-Thon" (B10 Large Conference Room A&B) || 09:00am - 12:00pm ||

|| '''LUNCH''' || 12:00pm - 01:30pm ||

|| Developer Working Sessions "Hack-A-Thon" (B10 Large Conference Room A&B) || 01:30pm - 04:00pm ||
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-=== Symposium Speakers ===
+'''[[/HackathonSchedule]]'''
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-[[http://www.utoronto.ca/boonelab/people/index.shtml|Charlie Boone, Ph.D.]]
+== Speakers ==
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-[[http://web.mit.edu/ki/about/leadership/friend.html|Dr. Stephen H. Friend, M.D., Ph.D.]]
+'''[[http://www.systemsbiology.org/scientists_and_research/faculty_groups/Hood_Group/Profile|Dr. Leroy Hood, M.D., Ph.D.]]'''
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-[[http://www.systemsbiology.org/scientists_and_research/faculty_groups/Hood_Group/Profile|Dr. Leroy Hood, M.D., Ph.D.]]
+Founder and President
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-Mark Newman
+Institute for Systems Biology
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+Line 73:
-Marc Vidal
+Seattle, Washington
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+'''[[http://web.mit.edu/ki/about/leadership/friend.html|Dr. Stephen H. Friend, M.D., Ph.D.]]'''



Co-founder, President, and Chief Executive Officer



Sage Bionetworks



'''[[http://www.utoronto.ca/boonelab/people/index.shtml|Dr. Charlie Boone, Ph.D.]]'''



Professor, Department of Medical Research 



Canada Research Chair Banting and Best



University of Toronto



'''[[http://www-personal.umich.edu/~mejn/|Dr. Mark Newman, Ph.D.]]'''



Paul Dirac Collegiate Professor of Physics



Professor, Center for the Study of Complex Systems



University of Michigan



'''[[http://www.ibbme.utoronto.ca/faculty/core/zandstra.htm|Dr. Peter Zandstra, Ph.D.]]'''



Professor, Canada Research Chair in Stem Cell Bioengineering



University of Toronto



'''[[http://ccmb.med.umich.edu/omenn|Dr. Gil Omenn]]'''



Professor of Internal Medicine, Human Genetics, and Public Health



Director, Center for Computational Medicine and Bioinformatics
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-http://www.hamptoninnannarbor.com/
+[[http://hamptoninn.hilton.com/en/hp/groups/personalized/ARBGRHX-CYT-20100717/index.jhtml|Cytoscape reservation group rate link - Hampton Inn]]
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-http://www.hiannarbor.com/
+[[http://www.ihg.com/h/d/HI/1/en/rates/ARBNC?groupBookingCode=CY1&_IATAno=99801505|Cytoscape reservation group rate link - Holiday Inn]]
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-== Event Sponsors ==
+== FAQ ==
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-'''Hosted by:'''
+'''Is there a poster session?'''
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-[[http://www.ncibi.org | The National Center for Integrative Biomedical Informatics]]
+Yes, there will be a poster sessions and reception from 5pm-6:30pm on Monday, July 19th.
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-[[http://ccmb.med.umich.edu | The Center for Computational Medicine and Bioinformatics]]
+'''How do I sign up for the poster session?'''
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+If you would like to submit an abstract for the poster session e-mail Jacki Troy (jtroy@umich.edu).
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+'''How do I sign up for the plugin demo?'''
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-'''The 2010 Cytoscape Retreat is generously sponsored by:'''
+If you would like to submit an abstract for the plugin demonstration e-mail Jacki Troy (jtroy@umich.edu).
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-{{attachment:agilentlogo-home.gif}}
+'''Will there be internet access at the retreat?'''



Yes, there will be free wireless access for all attendees.



'''Is there a discounted hotel rate?'''



Yes, we have negotiated group rates at both the Holiday Inn and Hampton Inn listed above.