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||<rowstyle="background-color:#FFEEAA;">'''MON October 9th'''||Gladstone Conference Rooms||
||9:00A
M-5:00PM||[:/Hackathon:Hackathon]||
||<rowstyle="background-color:#FFEEAA;">'''TUE October 10th'''||Gladstone Conference Rooms||
||9:00AM-5:00PM||[:/Hackathon:Hackathon]||
||<rowstyle="background-color:#FFEEAA;">'''WED October 11th'''||Gladstone Auditorium||
||10:00AM-4:00PM||Public Symposium||
|| ||Trey Ideker (UCSD, San Diego)||
|| ||Gary Bader (University of Toronto)[[BR]]''"BioPAX, cPath, and PDZ-based Protein Interaction Prediction"''||
|| ||Guy Warner (Unilever, UK)||
|| ||Ilya Schmulevich (ISB, Seattle)||
|| ||Benno Schwikowski (Institut Pasteur, Paris)||
|| ||TBA||
||<rowstyle="background-color:#FFEEAA;">'''THU October 12th'''||Genentech Hall Auditorium||
||9:00AM||Introductory Remarks and Summary of Hackathon||
||9:30AM||Cytoscape Process Brainstorm||
||11:00AM||Group Discussion on Major Development Tasks||
||12:00PM||BBQ Lunch on the Quad, plus recess||
||2:00PM||The Tao of Cytoscape: Overview||
||2:30PM||Plug-in & Usage Expo (part I)||
||3:30PM||Coffee Break||
||3:45PM||Plug-in & Usage Expo (part II)||
||6:00PM||Conference Dinner - TBA||
||<rowstyle="background-color:#FFEEAA;">'''FRI October 13th'''||Genentech Hall - Room N114||
||9:00AM||Discussion of Organizational and Funding Issues||
||10:30AM||Organize Major Development Tasks and Breakout||
||12:30PM||Lunch Breakout Groups Report||
||1:30PM||Cytoscape Users Meeting||
||2:30PM||Finalize Road Map and Elect new Core Developers||
||5:30PM||Dinner on own||
||<rowstyle="background-color:#FFEEAA;">'''SAT October 14th'''||In and Around San Francisco||
||Nature Tour||Hiking the Land's End trail with Bruce Conklin||
||Urban Tour||Discovering the historic/artistic murals with Allan Kuchinsky||
||Aqua Tour||Swimming in the Bay with Scooter Morris||
||<rowbgcolor="#ffeeaa">'''MON October 9th''' ||Gladstone Conference Rooms ||
||12:00P
M-5:00PM ||["/Hackathon"] ||
||<rowbgcolor="#ffeeaa">'''TUE October 10th''' ||Gladstone Conference Rooms ||
||9:00AM-5:00PM ||["/Hackathon"] ||
||<rowbgcolor="#ffeeaa">'''WED October 11th''' ||Gladstone Auditorium ||
||10:00AM-4:00PM ||Public Symposium ||
|| ||Trey Ideker (UCSD, San Diego) ||
|| ||Gary Bader (University of Toronto)[[BR]]''"BioPAX, cPath, and PDZ-based Protein Interaction Prediction"'' ||
|| ||Guy Warner (Unilever, UK) ||
|| ||Ilya Schmulevich (ISB, Seattle) ||
|| ||Benno Schwikowski (Institut Pasteur, Paris) ||
|| ||TBA ||
|| ||
||>4:00PM ||[:CytoscapeRetreat2006/Hackathon:Hackathon Extension]
||
||<rowbgcolor="#ffeeaa">'''THU October 12th''' ||Genentech Hall Auditorium ||
||9:00AM ||Introductory Remarks and Summary of Hackathon ||
||9:30AM ||Cytoscape Process Brainstorm ||
||11:00AM ||Group Discussion on Major Development Tasks ||
||12:00PM ||BBQ Lunch on the Quad, plus recess ||
||2:00PM ||The Tao of Cytoscape: Overview ||
||2:30PM ||Plug-in & Usage Expo (part I) ||
||3:30PM ||Coffee Break ||
||3:45PM ||Plug-in & Usage Expo (part II) ||
||6:00PM ||Conference Dinner - TBA ||
||<rowbgcolor="#ffeeaa">'''FRI October 13th''' ||Genentech Hall - Room N114 ||
||9:00AM ||Discussion of Organizational and Funding Issues ||
||10:30AM ||Organize Major Development Tasks and Breakout ||
||12:30PM ||Lunch Breakout Groups Report ||
||1:30PM ||Cytoscape Users Meeting ||
||2:30PM ||Finalize Road Map and Elect new Core Developers ||
||5:30PM ||Dinner on own ||
||<rowbgcolor="#ffeeaa">'''SAT October 14th''' ||In and Around San Francisco ||
||Nature Tour ||Hiking the Land's End trail with Bruce Conklin ||
||Urban Tour ||Discovering the historic/artistic murals with Allan Kuchinsky ||
||Aqua Tour ||Swimming in the Bay with Scooter Morris ||
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University of California San Francisco, UCSF, Mission Bay Campus: http://pub.ucsf.edu/missionbay/
[[BR]]J. David Gladstone Institutes, Mission Bay: http://www.gladstone.ucsf.edu/gladstone/site/missionbay/
[[BR]]Genentech Hall - N114: http://student.ucsf.edu/classrooms/classrooms/GEN%20-N114.html
[[BR]]Genentech Hall Auditorium: http://student.ucsf.edu/classrooms/classrooms/GenentechHallAuditorium.html
[[BR]]Gladstone Auditroium: attachment:Gladstone_Auditorium
University of California San Francisco, UCSF, Mission Bay Campus: http://pub.ucsf.edu/missionbay/ [[BR]]J. David Gladstone Institutes, Mission Bay: http://www.gladstone.ucsf.edu/gladstone/site/missionbay/ [[BR]]Genentech Hall - N114: http://student.ucsf.edu/classrooms/classrooms/GEN%20-N114.html [[BR]]Genentech Hall Auditorium: http://student.ucsf.edu/classrooms/classrooms/GenentechHallAuditorium.html [[BR]]Gladstone Auditroium: attachment:Gladstone_Auditorium
Line 57: Line 52:

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 [:/Hackathon:here].
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].
Line 61: Line 55:
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!]
[[BR]]If you have any problems email [mailto:scooter@cgl.ucsf.edu Scooter Morris] or [mailto:apico@gladstone.ucsf.edu Alex Pico]. 
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!] [[BR]]If you have any problems email [mailto:scooter@cgl.ucsf.edu Scooter Morris] or [mailto:apico@gladstone.ucsf.edu Alex Pico].
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Mission Bay Campus
University of California San Francisco
600 16th St.
San Francisco, CA 94158
Mission Bay Campus University of California San Francisco 600 16th St. San Francisco, CA 94158
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  * ''"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
  * ''"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
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  * 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
  * 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
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  * 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
  * 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
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  * ''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
  * ''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
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  * Great neighborhood, just 5 blocks from UCSF shuttle stop servicing Mission Bay
   * Very nice rooms
  * Great neighborhood, just 5 blocks from UCSF shuttle stop servicing Mission Bay
  * Very nice rooms
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   * Located 1 block from UCSF shuttle stop servicing Mission Bay
   * Very, very nice rooms
  * Located 1 block from UCSF shuttle stop servicing Mission Bay
  * Very, very nice rooms
== Travel ==
San Francisco is served by three airports: Sacremento 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. '''A''''''irport Shuttles:'''
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== Travel ==
Information comming soon...
 * 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
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Information comming soon... 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 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.

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

MON October 9th

Gladstone Conference Rooms

12:00PM-5:00PM

["/Hackathon"]

TUE October 10th

Gladstone Conference Rooms

9:00AM-5:00PM

["/Hackathon"]

WED October 11th

Gladstone Auditorium

10:00AM-4:00PM

Public Symposium

Trey Ideker (UCSD, San Diego)

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

Guy Warner (Unilever, UK)

Ilya Schmulevich (ISB, Seattle)

Benno Schwikowski (Institut Pasteur, Paris)

TBA

>4:00PM

[:CytoscapeRetreat2006/Hackathon:Hackathon Extension]

THU October 12th

Genentech Hall Auditorium

9:00AM

Introductory Remarks and Summary of Hackathon

9:30AM

Cytoscape Process Brainstorm

11:00AM

Group Discussion on Major Development Tasks

12:00PM

BBQ Lunch on the Quad, plus recess

2:00PM

The Tao of Cytoscape: Overview

2:30PM

Plug-in & Usage Expo (part I)

3:30PM

Coffee Break

3:45PM

Plug-in & Usage Expo (part II)

6:00PM

Conference Dinner - TBA

FRI October 13th

Genentech Hall - Room N114

9:00AM

Discussion of Organizational and Funding Issues

10:30AM

Organize Major Development Tasks and Breakout

12:30PM

Lunch Breakout Groups Report

1:30PM

Cytoscape Users Meeting

2:30PM

Finalize Road Map and Elect new Core Developers

5:30PM

Dinner on own

SAT October 14th

In and Around San Francisco

Nature Tour

Hiking the Land's End trail with Bruce Conklin

Urban Tour

Discovering the historic/artistic murals with Allan Kuchinsky

Aqua Tour

Swimming in the Bay with Scooter Morris

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:

Travel

San Francisco is served by three airports: Sacremento 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. Airport Shuttles:

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 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.

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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