Cytoscape Developer Retreat 2006

San Francisco - October 9th - 14th, 2006 Register Now!

The 4th Annual Cytoscape Retreat will be held October 11th - 13th, 2006 (Wed-Fri) at UCSF Mission Bay Campus in San Francisco. The retreat will be preceded by a 2-day Hackathon on the 9th and 10th. And, if you can stay another day, there will be recreational activities organized for Saturday the 14th.

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 of Systems Biology, Seattle), and Annette Adler (Agilent Technologies, Santa Clara, CA). This year the retreat will be co-hosted by two new contributor groups of Tom Ferrin (UCSF Computer Graphics Laboratory) and Bruce Conklin (Gladstone/UCSF, GenMAPP).

The meeting 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 code. Cytoscape-related presentations by invitees are welcome. Social activities around the meeting are also scheduled. This is a great chance to influence the development direction of Cytoscape.

We've added a public symposium this year to take advantage of the large number of institutions in the Bay Area with a significant interest in systems biology and the network visualization of biological data. Our goal is to invite presentations to provide attendees with an overview of Cytoscape as a tool and (more importantly) some of the areas of science that it is being applied to. We will be forming a "program committee" in the next couple of weeks, so if you have any great ideas, please send e-mail to Alex Pico or Scooter Morris.

Preliminary Schedule

MON October 9th

Gladstone Conference Rooms A & B



5:30 PM

tour of local campus, then dinner on own

TUE October 10th

Gladstone Conference Rooms C & D (excluding 11:30-1:30)



11:30PM or 1:30PM

box lunch, then optional visit to Mission Bay Visitor Center

WED October 11th

Gladstone Auditorium

Public Symposium

Network-Based Approaches to Biological Data Integration and Analysis


Perspective by Guy Warner (Unilever, UK)


Patricia Babbitt (QB3/UCSF, San Francisco)
"Network Analysis Reveals New Relationships among Divergent Proteins Missed by Tree-Based Approaches"


Gary Bader (University of Toronto)
"BioPAX, cPath, and PDZ-based Protein Interaction Prediction"


Lunch Break - catered by Moffitt


Mirit Aladjem (National Cancer Inst, NIH)
"Molecular Interaction Maps of Biological Signalling Networks"


Ilya Shmulevich (ISB, Seattle)
"Data Integration and Genetic Network Modeling"


Break - coffee and light snacks


Benno Schwikowski (Institut Pasteur, Paris)
"Mass Spec Informatics: Towards Dense Protein Expression Networks"


Trey Ideker (UCSD, San Diego)
"Protein Network Comparative Genomics"


Hackathon Extension


6:00PM SAB & Board of Directors Meeting at Gladstone conference Room 403, takeout Thai food

THU October 12th

Genentech Hall Auditorium (Meeting Notes)


Introductory Remarks and Summary of Hackathon


MIMs Discussion


Birds of Feather Sessions


BBQ Lunch on the Quad, plus recess


The Tao of Cytoscape: Overview and Context for Expo


Plugin & Usage Expo (part I)


Coffee Break


Plugin & Usage Expo (part II)


Conference Dinner - Goat Hill Pizza, 300 Connecticut at 18th Street all you can eat and drink

FRI October 13th

Genentech Hall - Room N114


Cytoscape 2.4 rundown


Organize Major Development Tasks and BreakoutGroups


Working Lunch - Burritos


BreakoutGroups Report


Parallel session of Board of Directors and SAB to discuss vision (Gladstone rm 403)


Work on RoadMap2006 / Match Core Developers to Action Items


Wrap-up: SAB Input, Board Issues & Future Vision


Dinner on own


Option for de Young Museum Event

SAT October 14th

In and Around San Francisco


AM Hiking SF Coastal Trail to Land's End Beach with Bruce Conklin trail map


AM Touring the historic Mission District murals with Allan Kuchinsky:


AM Swimming in the Bay with Scooter Morris

Campus & Conference Rooms

University of California San Francisco, UCSF, Mission Bay Campus:
J. David Gladstone Institutes, Mission Bay:
Genentech Hall - N114:
Genentech Hall Auditorium:
Gladstone Auditorium: Gladstone_Auditorium


October 9 and 10th, 2006, (Mon-Tues) at Mission Bay, UCSF, developers will have the opportunity to play with code pre-meeting. If you are interested in taking part in the Hackathon then be sure to plan accordingly (i.e., 2-days earlier) and indicate your interest in your registration. Find more information on Hackathon topics here.


This is a free event. Please use our online registration system: Register Now!
If you have any problems email Scooter Morris or Alex Pico.


Mission Bay Campus University of California San Francisco 600 16th St. San Francisco, CA 94158

Hotel Suggestions

October is a big conference month in San Francisco. We highly recommend making your reservations ASAP! Try or check out these options below:


We recommend San Francisco International Airport (SFO), as it is easily accessible to the city, and has numerous shuttles, taxis, car services and public transportation that serve all of its terminals. Your San Francisco hotel may be able to provide complimentary shuttle service to and from the airport. Car rentals are also available at the airport, with complimentary shuttle service to their rental facilities.

For more information regarding San Francisco International Airport, including maps of its terminals, visit their website:

Transportation A number of shuttle services provide transportation to and from the airport. Any of the following agencies provide shuttle service that is easily accessible from any airport terminal, or hotel in San Francisco.

Public transportation, (Muni and BART), is easily accessible from the airport to anywhere within the city.

Airport Shuttles:

Taxi Services- From the airport, and within San Francisco: *Fare from SFO to the city will range from $35-50

Public transportation services in San Francisco, including fares, routes, and schedules: Transit 511 Weblink:

UCSF Mission Bay Shuttle Service - Free Service! UCSF provides free shuttle service from to and from all of its campuses throughout San Francisco, and public transportation. For more information and schedules, vist the weblink to the UCSF transportation website:

Example Trip Planner

San Francisco Tourism

San Francisco boasts a rich multi-cultural history, and is a beautiful city with many local and area attractions that appeal to just about any type of traveler. While you are here, be sure to take in a few sights, and experience this unique city, or perhaps some of the beautiful attractions nearby, including Sausalito, Muir Woods, California wine country, or Alcatraz. Included below are some useful links to help you plan your visit to many of the local attractions. We hope you enjoy your visit to our great city!

CytoscapeRetreat2006 (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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