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= Cytoscape Developer Retreat 2010 = == July 18th-20th, 2010 == == U-M North Campus Research Complex, Ann Arbor, Michigan == |
== Cytoscape Developer Retreat 2010 == '''July 18th-20th, 2010 - ONLINE REGISTRATION CLOSED''' - For late registration E-mail Jacki Troy(jtroy@umich.edu) |
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| 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 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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== Schedule == === Sunday, July 18, 2010 === || 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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= Tentative Schedule = == Sunday, July 18, 2010 == || 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 || |
=== 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'' || 08:30am - 08:45am || || Lee Hood, M.D., Ph.D. - ''P4 Medicine: Catalyzing a Revolution from Reactive to Proactive Medicine ''|| 08:45am - 09:30am || || Charlie Boone, Ph.D. - ''The Genetic Landscape of a Cell''|| 09:30am - 10:15am || || '''BREAK''' || 10:15am - 10:25am || || Mark Newman, Ph.D. - ''Social Networks and the Spread of Infectious Disease'' || 10:30am - 11:15am || || Eric Neuman, Ph.D. - ''Visual Analysis of the Web of Linked Data: the S*QL Plugin for Cytoscape'' || 11:15am - 12:00pm || || '''LUNCH''' || 12:00pm - 01:00pm || || Edward Rietman, Ph.D. - ''Observation of spatial protein-protein interactome dynamics in Arabidopsis root '' || 01:00pm - 01:45pm || || Peter Zandstra, Ph.D. || 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'' || 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'' || 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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== Monday, July 19, 2010 == || 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 || |
=== 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 || |
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== Tuesday, July 20, 2010 == || 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 || |
'''[[/HackathonSchedule]]''' |
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| == Symposium Speakers == | == Speakers == |
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| Charlie Boone | '''[[http://www.systemsbiology.org/scientists_and_research/faculty_groups/Hood_Group/Profile|Dr. Leroy Hood, M.D., Ph.D.]]''' |
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| [[http://web.mit.edu/ki/about/leadership/friend.html|Dr. Stephen H. Friend, M.D., Ph.D.]] | Founder and President |
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| [[http://www.systemsbiology.org/scientists_and_research/faculty_groups/Hood_Group/Profile|Dr. Leroy Hood, M.D., Ph.D.]] | Institute for Systems Biology |
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| Mark Newman | Seattle, Washington |
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| Marc Vidal | '''[[http://web.mit.edu/ki/about/leadership/friend.html|Dr. Stephen H. Friend, M.D., Ph.D.]]''' |
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| Co-founder, President, and Chief Executive Officer | |
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| = Location & Info = | Sage Bionetworks |
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| The Cytoscape retreat will be held at the [[http://www.umich.edu|University of Michigan]], North Campus Research Complex in Ann Arbor, Michigan. |
'''[[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 == Location & Info == The Cytoscape retreat will be held at the [[http://www.umich.edu|University of Michigan]], North Campus Research Complex in Ann Arbor, Michigan. [[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=2800+Plymouth+Road,+Ann+Arbor,+MI&sll=42.305618,-83.702656&sspn=0.006705,0.008991&ie=UTF8&hq=&hnear=2800+Plymouth+Rd,+Ann+Arbor,+Washtenaw,+Michigan+48105&ll=42.302547,-83.705832&spn=0.006705,0.008991&t=h&z=17|Google Map]] {{http://portal.ncibi.org/gateway/NCRCMap.jpeg}} |
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| = Travel and Accommodation = | == Travel and Accommodation == |
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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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| '''Hampton Inn''' - $92.00/night | '''Hampton Inn''' - $92.00/night (Group code: CYT) |
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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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2300 Green Road Ann Arbor, MI 48105 |
2300 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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3600 Green Road Ann Arbor, MI 48105 |
3600 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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| [[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. |
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
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 |
08:30am - 08:45am |
Lee Hood, M.D., Ph.D. - P4 Medicine: Catalyzing a Revolution from Reactive to Proactive Medicine |
08:45am - 09:30am |
Charlie Boone, Ph.D. - The Genetic Landscape of a Cell |
09:30am - 10:15am |
BREAK |
10:15am - 10:25am |
Mark Newman, Ph.D. - Social Networks and the Spread of Infectious Disease |
10:30am - 11:15am |
Eric Neuman, Ph.D. - Visual Analysis of the Web of Linked Data: the S*QL Plugin for Cytoscape |
11:15am - 12:00pm |
LUNCH |
12:00pm - 01:00pm |
Edward Rietman, Ph.D. - Observation of spatial protein-protein interactome dynamics in Arabidopsis root |
01:00pm - 01:45pm |
Peter Zandstra, Ph.D. |
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 |
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 |
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 |
Speakers
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
Professor, Department of Medical Research
Canada Research Chair Banting and Best
University of Toronto
Paul Dirac Collegiate Professor of Physics
Professor, Center for the Study of Complex Systems
University of Michigan
Professor, Canada Research Chair in Stem Cell Bioengineering
University of Toronto
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.