Cytoscape Developer Retreat 2010

July 18th-20th, 2010 - ONLINE REGISTRATION CLOSED - For late registration E-mail Jacki Troy(

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

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 (

Download Cytoscape Retreat Flyer


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


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


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


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 S*QL Plugin for Cytoscape Watch Video

11:15am - 12:00pm


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


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


Board of Director's Dinner


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


12:00pm - 01:30pm

Developer Working Sessions "Hack-A-Thon" (B10 Large Conference Room A&B)

01:30pm - 04:00pm



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:

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


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


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 (

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 (

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.


CytoscapeRetreat2010 (last edited 2010-08-11 16:28:53 by alsace)

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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