Cytoscape Developer Retreat 2005

San Diego - November 30 - December 1st, 2005

The 3rd Annual Cytoscape Retreat will be held November 30 and December 1st, 2005 (Wed-Thurs) at UCSD in San Diego.

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) and Lee Hood (Institute of Systems Biology, Seattle).

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.

Schedule

DATE

EVENT, University of California, San Diego (UCSD)

Mon-Tue November 28-29

Hackathon

WED NOVEMBER 30th

Multi-media room, CAL-IT2 (UCSD)

9:00AM

Introductory Remarks

9:30AM

RFC-2 Cytoscape Process Brainstorm with break

11:00AM

Group discussion on major development tasks

12:00PM

Lunch on own

1:30PM

Organize into breakout groups surrounding development tasks, (Rms 2004, 2006, 3004)

3:00PM-3:15PM

Coffee Break

3:15PM

Plug-in & User-experience Expo

6:00PM

Conference Dinner (Epazote, Del Mar) http://www.epazote.signonsandiego.com/1.html

THU DECEMBER 1st

Multi-media room, CAL-IT2 (UCSD)

9:00AM

Discussion of Organizational and Funding Issues (chaired by Louis Coffman, Vice-President/COO, The Institute for Systems Biology)

10:30AM

Hike in Torrey Pines Nature Reserve

12:30PM

Lunch Breakout groups report,(Rms 2004, 2006, 3004)

1:30PM

Business Meetings

[parallel]

Cytoscape Users Meeting

[parallel]

Cytoscape Board of Directors Meeting

2:30PM

Finalize Road Map and Elect new Core Developers

5:30PM

Dinner on own

Fri-Sat December 2-3

RECOMB Systems Biology Satellite Conference (CAL-IT2)

Hackathon

November 28 and 29th, 2005, (Mon-Tues) at UCSD, developers will have the opportunity to play with code pre-meeting. If you are interested in taking part in the Hackathon then email Michael Smoot (msmoot@ucsd.edu) with your planned arrival and contact details. Please put "Cystoscape Hackathon" in the subject field of the email.

Registration

This is a free event. To register for the conference, send the following information via email to [msmoot@ucsd.edu]. Please put "Cytoscape Registration" in the subject field of the email.

2005 CYTOSCAPE RETREAT Registration Form

Name:

Affiliation:

Email:

URL (optional):

Mailing Address:

Phone Number:

Fax Number:

Category: [ ] Student [ ] Faculty [ ] Industry [ ] Government

Location

Multi-media room, CAL-IT2 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92130

http://www.calit2.net/about/buildings/index.php

http://www.ucsd.edu/visit/directions.html

Take Interstate 5 SOUTH EXIT on GENESEE AVENUE west. Proceed to the third light at the top of the hill. TURN LEFT onto NORTH TORREY PINES ROAD. TURN LEFT onto NORTH POINT DRIVE and continue until you see a UCSD Visitor Information Center on the right.

Take Interstate 5 NORTH EXIT on GILMAN DRIVE. TURN LEFT at the light onto Gilman Drive. Continue for about 1 1/2 miles until you see a UCSD Visitor Center on the right.

You may obtain specific directions, visitor parking information and a campus map at the UCSD Visitor Center. Parking permits are availbel for $6 per day at several locatios around campus: http://blink.ucsd.edu/Blink/External/Topics/Policy/0,1162,11776,00.html

RECOMB 2005 Conferences and Call for Papers

Focused RECOMB Satellite events on topics of particular interest to the computational biology community, are being held at UCSD, 2-4 December 2005.

The RECOMB Satellite Conference on Systems Biology will be held in conjunction with the 2nd RECOMB Satellite Conference on Regulatory Genomics. This year's conferences will also include a special session on Developmental Biology. The joint program features an exciting group of invited speakers, presentations of accepted abstracts, and opportunities for discussion. More information about speakers and each of these events can be found at: http://research.calit2.net/recomb-workshop05

A Call for Papers has been sent out, soliciting original, previously unpublished research results (including significant work-in-progress) or state-of-the-art surveys in all aspects of systems biology and regulation. Extended abstracts should be sent by email to recomb-workshop@cs.ucsd.edu. Submissions must be received in electronic form by 11:59pm (PDT) of October 15, 2005 for your submission to be considered. Please see the url above for more details.

Hotel

Radisson Hotel La Jolla 3299 Holiday Court, La Jolla California 92037, US

Estancia La Jolla Hotel & Spa 9700 N. Torrey Pines Road, La Jolla, California 92037

Hyatt Regency La Jolla at Aventine 3777 La Jolla Village Drive, San Diego, California, 92122

Travel

San Diego is served by San Diego International Airport (SAN) UCSD is located in La Jolla approximately 12 miles from the San Diego International Airport (also called Lindbergh Field) and downtown San Diego. Airport shuttles, taxis and car rentals can be found at all terminals. If you have a hotel reservation in San Diego, some hotels provide complimentary shuttle services to and from the airport. Car rentals are also available at the airport with shuttles providing transportation to the rental facilities.

A number of companies operate shuttle vans. Cloud 9 shuttle (http://www.cloud9shuttle.com) will provide service between Warren College at UCSD and the airport for $23.50 each way. Shuttle Service is available on the Transportation Plazas across from Terminals 1 and 2 via the skybridge. If you find yourself arriving at the Transportation Plaza with at least 5 other Cystoscape-bound persons, ask Cloud 9 for an "exclusive rate", which can reduce costs up to $4 per person off the fare.

Maps of the airport and additional information can be found on the San Diego International Airport's web page http://www.san.org/airport/

Train information and fares can be found via the Metropolitan Transit System at: http://www.sdcommute.com/RiderInfo/tripPlanning/index.asp Both the train (Amtrak) and bus (Greyhound) stations are located in downtown San Diego, not far from the airport. Cloud 9 Shuttle (http://www.cloud9shuttle.com) will provide service from either station to UCSD. Call them at 619-505-4950 or 800-9-SHUTTLE.

Taxi fare is approximately $40-$50 each way to or from the airport, bus station, or train depot. The following providers can be contacted for additional information and reservations.

Airport Yellow Cab of San Diego: 619- 234-6161 Red Top Cab: 619-531-1111 San Diego Co-Op Cab: 619-280-5555

For local La Jolla transportation, contact: La Jolla Cab Co. at 858-453-4222.

By car From north of La Jolla, take Interstate 5 SOUTH EXIT on GENESSEE AVENUE west. Proceed to the third light at the top of the hill. TURN LEFT onto NORTH TORREY PINES ROAD. TURN LEFT onto NORTH POINT DRIVE. Continue until you see a UCSD Visitor Information Center on the right. You may obtain specific directions, visitor parking information and a campus map at the UCSD Visitor Center.

From south of La Jolla, take Interstate 5 NORTH EXIT on GILMAN DRIVE. TURN LEFT at the light onto Gilman Drive. Continue for about 1-½ miles until you see a UCSD Visitor Center on the right. You may obtain specific directions, visitor parking information and a campus map at the UCSD Visitor Center.

San Diego tourism

San Diego is a much smaller city than Chicago, but there is still plenty to do, not forgetting the beaches of course (there are several nearby).

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