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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)	10:00am - 12:00noon
LUNCH	12:00 - 01:30pm
Plugin Demonstrations	01:30pm - 05:30pm
Giovanni Scardoni - Analyzing biological networks with CentiScaPe
Sasha Tkachev - Web Service Client and Server for PhosphoSitePlus database
Kozo Nishida - Importing KEGG pathway and mapping custom node graphics on Cytoscape (Project Web Site)
Morgan Taschuk - CID: Exploring Interactomes with Cytoscape
Terry Weymouth - Metscape Plugin for Visualization and Analysis of Genes and Metabolites
Gregory Hannum - A Cytoscape plugin for Physical and Genetic Interaction Alignment – PanGIA
James Vlasblom - Ortho-Nets: Simultaneous analysis and visualization of protein-interaction network environments of orthologous genes in different organisms
Jochen Weile - Concise visualizations of integrated datasets with the OndexView Cytoscape plug-in
Jason Montojo - GeneMANIA Cytoscape Plugin: Fast desktop gene function prediction
Ruth Isserlin - Enrichment Map: A Cytoscape Plugin to enable visualization and interpretation of Gene-Set Enrichment Analysis
Terry Weymouth - The Cytoscape MiMI Plugin with the NCIBI/MiMI Attribute Browser
Gang Su - Cytoscape plug-ins: GLay v.2 and GSearcher
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
Welcome - Dr. Brian Athey / Dr. Gil Omenn	08:30am - 08:45am
Speaker - Lee Hood, M.D., Ph.D.	08:45am - 09:30am
Speaker - Charlie Boone, Ph.D.	09:30am - 10:15am
BREAK	10:15am - 10:25am
Speaker - Mark Newman, Ph.D.	10:30am - 11:15am
Speaker - Eric Neuman, Ph.D.	11:15am - 12:00pm
LUNCH	12:00pm - 01:00pm
Speaker - Edward Rietman	01:00pm - 01:45pm
Speaker - Peter Zandstra, Ph.D.	01:45pm - 02:30pm
BREAK	02:30pm - 02:40pm
Speaker - Nevan Krogan, Ph.D.	02:45pm - 03:30pm
Speaker - Brian Athey, Ph.D.	03:30pm - 04:00pm
Speaker - Stephen Friend, M.D., Ph.D.	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, 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)'''
-Line 13:
+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)|| 10:00am - 12:00noon ||

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

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

|| Giovanni Scardoni - ''Analyzing biological networks with CentiScaPe''|| ||

|| Sasha Tkachev - ''Web Service Client and Server for PhosphoSitePlus database'' || ||

|| Kozo Nishida - ''Importing KEGG pathway and mapping custom node graphics on Cytoscape'' ([[http://code.google.com/p/kgmlreader/|Project Web Site]]) || ||

|| Morgan Taschuk - ''CID: Exploring Interactomes with Cytoscape'' || ||

|| Terry Weymouth - ''Metscape Plugin for Visualization and Analysis of Genes and Metabolites'' || ||

|| Gregory Hannum - ''A Cytoscape plugin for Physical and Genetic Interaction Alignment – PanGIA'' || ||

|| James Vlasblom - ''Ortho-Nets: Simultaneous analysis and visualization of protein-interaction network environments of orthologous genes in different organisms'' || ||

|| Jochen Weile - ''Concise visualizations of integrated datasets with the OndexView Cytoscape plug-in'' || ||

|| Jason Montojo - ''GeneMANIA Cytoscape Plugin: Fast desktop gene function prediction'' || ||

|| Ruth Isserlin - ''Enrichment Map: A Cytoscape Plugin to enable visualization and interpretation of Gene-Set Enrichment Analysis'' || ||

|| Terry Weymouth - ''The Cytoscape MiMI Plugin with the NCIBI/MiMI Attribute Browser''|| ||

|| Gang Su - ''Cytoscape plug-ins: GLay v.2 and GSearcher'' || ||

|| '''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 ||

|| Welcome - Dr. Brian Athey / Dr. Gil Omenn || 08:30am - 08:45am ||

|| Speaker - Lee Hood, M.D., Ph.D. || 08:45am - 09:30am ||

|| Speaker - Charlie Boone, Ph.D. || 09:30am - 10:15am ||

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

|| Speaker - Mark Newman, Ph.D. || 10:30am - 11:15am ||

|| Speaker - Eric Neuman, Ph.D. || 11:15am - 12:00pm ||

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

|| Speaker - Edward Rietman || 01:00pm - 01:45pm ||

|| Speaker - Peter Zandstra, Ph.D. || 01:45pm - 02:30pm ||

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

|| Speaker - Nevan Krogan, Ph.D. || 02:45pm - 03:30pm ||

|| Speaker - Brian Athey, Ph.D. || 03:30pm - 04:00pm ||

|| Speaker - Stephen Friend, M.D., Ph.D. || 04:00pm - 05:00pm ||

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

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

|| '''Board of Director's Dinner''' || 06:30pm ||
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+Line 59:
-|| 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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+Line 66:
-Charlie Boone
+== Speakers ==
-Line 39:
+Line 68:
-[[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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+Line 70:
-[[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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+Line 72:
-Mark Newman
+Institute for Systems Biology
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+Line 74:
-Marc Vidal
+Seattle, Washington
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+Line 76:
+'''[[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://portal.ncibi.org/gateway/NCRCMap.jpeg}}
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-We recommend the Detroit Metro Airport if you are flying in.
+=== Air Travel ===



We recommend the [[http://www.metroairport.com/| Detroit Metro Airport (DTW)]] if you are flying in. 



For transport to and from the airport see: [[http://www.customtransit.com/|Custom Transit]] or [[http://www.metrocars.com/|Metro Cars]]



=== Hotels ===
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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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-Green Road

Ann Arbor, MI 48105
+Green Road, Ann Arbor, MI 48105
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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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-Green Road

Ann Arbor, MI 48105
+Green Road, Ann Arbor, MI 48105
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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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+Line 152:
-[[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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+Line 154:
+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.