Cytoscape Developer Retreat 2006

San Francisco - October 9th - 14th, 2006

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 [mailto:apico@gladstone.ucsf.edu Alex Pico] or [mailto:scooter@cgl.ucsf.edu Scooter Morris].

Preliminary Schedule

Campus & Conference Rooms

University of California San Francisco, UCSF, Mission Bay Campus: http://pub.ucsf.edu/missionbay/ BRJ. David Gladstone Institutes, Mission Bay: http://www.gladstone.ucsf.edu/gladstone/site/missionbay/ BRGenentech Hall - N114: http://student.ucsf.edu/classrooms/classrooms/GEN%20-N114.html BRGenentech Hall Auditorium: http://student.ucsf.edu/classrooms/classrooms/GenentechHallAuditorium.html BRGladstone Auditroium: attachment:Gladstone_Auditorium

Hackathon

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 [:CytoscapeRetreat2006/Hackathon:here].

Registration

This is a free event. Please use our online registration system: [http://www.cgl.ucsf.edu/cgi-bin/surveyCGI.py?../datadocs/Workshops/CytoscapeRetreat/wsReg.xml Register Now!] BRIf you have any problems email [mailto:scooter@cgl.ucsf.edu Scooter Morris] or [mailto:apico@gladstone.ucsf.edu Alex Pico].

Location

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

http://pub.ucsf.edu/missionbay/

Hotel Suggestions

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

• $ [http://www.thepowellhotel.com/ The Powell Hotel] --> [http://maps.google.com/maps?f=q&hl=en&q=28+Cyril+Magnin+St,+San+Francisco,+CA map]

  • "Official" Cytoscape Developer's Pick!

  • Conveniently located at the Powell BART station, 1 block from the UCSF shuttle stop servicing Mission Bay
  • Decent sized rooms, simply decorated
  • Cafe Powell is located in the lobby
  • Free wireless in all rooms

• $ [http://www.hotelmarktwain.com/ Hotel Mark Twain] --> [http://maps.google.com/maps?f=q&hl=en&q=345+Taylor+St,+San+Francisco,+CA map]

  • Located 4 blocks from the UCSF shuttle stop servicing Mission Bay
  • Small but warmly decorated rooms, lobby, bar
  • Popular Sultan Indian Restaurant in the lobby
  • Exercise room
  • Wireless access for $9.95 per 24-hour period

• $ [http://www.hotelastoria-sf.com/ Hotel Astoria] - [http://maps.google.com/maps?f=q&hl=en&q=510+Bush+St,+San+Francisco,+CA map]

  • Located 3 blocks from the UCSF shuttle stop servicing Mission Bay
  • Located at the famous gates of Chinatown!
  • Decent sized rooms, not really decorated
  • Continental breakfast included
  • No wireless available

• $ [http://www.jdvhospitality.com/hotels/hotel/248 Hotel Carlton] - [http://maps.google.com/maps?f=q&hl=en&q=1075+Sutter+St,+San+Francisco,+CA map]

  • Not conveniently located in the Tenderloin district (think, sketchy)

  • Transportation: 47 bus on Van Ness to CalTrans Station, then UCSF shuttle service to Mission Bay

  • Beautiful, large rooms and lobby - very nice
  • Internet access in some public areas; pay for room access

• $$ [http://www.cartwrighthotel.com/ Cartwright Hotel] - [http://maps.google.com/maps?f=q&hl=en&q=524+Sutter+St,+San+Francisco,+CA map]

  • Great neighborhood, just 5 blocks from UCSF shuttle stop servicing Mission Bay
  • Very nice rooms

• $$$ [http://www.hotelpalomar.com/ Hotel Palomar] - [http://maps.google.com/maps?f=q&hl=en&q=12+fourth+St,+San+Francisco,+CA map]

  • Located 1 block from UCSF shuttle stop servicing Mission Bay
  • Very, very nice rooms

Travel

San Francisco is served by three airports: Sacramento International (SMF), Oakland (OAK), and San Francisco International (SFO). We recommend San Francisco International Airport (SFO), as it is easily accessible to the city, and has numerous shuttles, taxis and car services 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: http://www.flysfo.com/

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.

• http://www.bart.gov/guide/airport/sfo.asp

Airport Shuttles:

• Super Shuttle Service: http://www.supershuttle.com/htm/cities/sfo.htm

• Additional links to other available private and public transportation and shuttles : http://www.sftravel.com/shutl.html

Taxi Services- From the airport, and within San Francisco: http://www.zpub.com/sf/zsf-taxi.html *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: http://transit.511.org/index.asp

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: http://www.campuslifeservices.ucsf.edu/transportation/shuttles/timetables/default.php

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!

• http://onlyinsanfrancisco.com/ A full service guide and a good starting point for any visitor to San Francisco; includes restaurant listings, local events and links to tours and points of interest throughout the city.

• http://www.buysanfranciscotours.com/ A useful link for checking into sightseeing and adventure tours available within the city of San Francisco, including cable car and trolley tours, as well as tours to Alcatraz, Muir Woods, and beautiful California wine country.

• http://www.sfcablecar.com/ Your guide for planning a ride on one of San Francisco's famed historic cable cars. Includes routes and rates.

• http://www.sfzoo.org/ A link to our zoo, located within the San Francisco city limits.

• http://www.sfmission.com/entertain/webguide.htm A useful link for information and links to museums in San Francisco, including the San Francisco Museum of Modern Art and the DeYoung Museum.

• http://www.pier39.com/Media/MediaKit/profile.htm - official website for San Francisco's famous Pier 39 and Fisherman's Wharf - Famed Ghiradelli square is just steps away.

• http://www.ghiradellisq.com - Official website to this historic landmark, including its famous chocolate shop and specialty stores and restaurants.