Cytoscape Wiki
Cytoscape Retreat 2007
Amsterdam; the Netherlands - November 6th - 9th, 2007
This is a preliminary set-up for the retreat 2007. Consider it a kind of RFC for the coming month or so; any suggestions changes are welcome! The only date that's pretty much fixed is the symposium date; than is the only time a big conference room is available. In the current scenario (CytoRetreat2007Planning : due in a few days) a first announcement will be sent at the beginning of april; so that should be the end of RFC status.
The 5th Annual Cytoscape Retreat will be held November 6th - 9th, 2006 (Tue-Fri) at the [http://www.amc.nl/ Academic Medical Center] of the University of Amsterdam in the Netherlands. [http://maps.google.com/maps?f=q&hl=en&q=Academisch+Medisch+Centrum,+Amsterdam,+North+Holland,+Netherlands&ie=UTF8&sll=52.373922,4.958954&sspn=0.178998,0.466919&z=11&ll=52.32275,4.957581&spn=0.179205,0.692139&om=1&iwloc=addr map]
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.
Preliminary Schedule
MON October 9th |
Gladstone Conference Rooms A & B |
12:00PM-5:00PM |
["/Hackathon"] |
5:30 PM |
tour of local campus, then dinner on own |
TUE October 10th |
Gladstone Conference Rooms C & D (excluding 11:30-1:30) |
9:00AM-5:00PM |
["/Hackathon"] |
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 |
10:00AM-10:15AM |
Perspective by Guy Warner (Unilever, UK) BRattachment:CytoscapeRetreat2006/Symposium/GuyWarner_CytoscapeSymposium2006.ppt |
10:15AM-11:00AM |
[:CytoscapeRetreat2006/Symposium:Patricia Babbitt] (QB3/UCSF, San Francisco) BR"Network Analysis Reveals New Relationships among Divergent Proteins Missed by Tree-Based Approaches" |
11:00AM-11:45PM |
[:CytoscapeRetreat2006/Symposium:Gary Bader] (University of Toronto)BR"BioPAX, cPath, and PDZ-based Protein Interaction Prediction" BRattachment:CytoscapeRetreat2006/Symposium/GaryBader_CytoscapeSymposium2006.ppt |
11:45PM-12:45PM |
Lunch Break - catered by Moffitt |
12:45PM-1:30PM |
[:CytoscapeRetreat2006/Symposium:Mirit Aladjem] (National Cancer Inst, NIH)BR "Molecular Interaction Maps of Biological Signalling Networks" BRattachment:CytoscapeRetreat2006/Symposium/MiritAladjem_CytoscapeSymposium2006.ppt |
1:30PM-2:15PM |
[:CytoscapeRetreat2006/Symposium:Ilya Shmulevich] (ISB, Seattle)BR"Data Integration and Genetic Network Modeling" BRattachment:CytoscapeRetreat2006/Symposium/IlyaShmulevich_CytoscapeSymposium2006.pdf |
2:15PM-2:30PM |
Break - coffee and light snacks |
2:30PM-3:15PM |
[:CytoscapeRetreat2006/Symposium:Benno Schwikowski] (Institut Pasteur, Paris)BR"Mass Spec Informatics: Towards Dense Protein Expression Networks" |
3:15PM-4:00PM |
[:CytoscapeRetreat2006/Symposium:Trey Ideker] (UCSD, San Diego)BR"Protein Network Comparative Genomics" |
|
|
>4:00PM |
[:CytoscapeRetreat2006/Hackathon:Hackathon Extension] |
Dinner |
6:00PM SAB & Board of Directors Meeting at Gladstone conference Room 403, takeout Thai food |
THU October 12th |
Genentech Hall Auditorium ([:/UserMeetingNotes:Meeting Notes]) |
9:00AM |
Introductory Remarks and Summary of Hackathon |
9:45AM |
MIMs Discussion |
11:00AM |
Birds of Feather Sessions |
12:00PM |
BBQ Lunch on the Quad, plus recess |
2:00PM |
The Tao of Cytoscape: Overview and Context for Expo |
2:30PM |
[:CytoscapeRetreat2006/Plugins:Plugin & Usage Expo] (part I) |
3:30PM |
Coffee Break |
3:45PM |
[:CytoscapeRetreat2006/Plugins:Plugin & Usage Expo] (part II) |
6:00PM |
Conference Dinner - Goat Hill Pizza, 300 Connecticut at 18th Street all you can eat and drink |
FRI October 13th |
Genentech Hall - Room N114 |
9:30AM |
Cytoscape 2.4 rundown |
10:30AM |
Organize Major Development Tasks and BreakoutGroups |
12:30PM |
Working Lunch - [http://en.wikipedia.org/wiki/Burritos Burritos] |
1:00PM |
BreakoutGroups Report |
1:00PM |
Parallel session of Board of Directors and SAB to discuss vision (Gladstone rm 403) |
3:00PM |
Work on RoadMap2006 / Match Core Developers to Action Items |
5:00PM |
Wrap-up: SAB Input, Board Issues & Future Vision |
5:45PM |
Dinner on own |
>5:30PM |
Option for de Young Museum Event http://www.thinker.org/deyoung/calendar/day.asp?day=10/13/2006 |
SAT October 14th |
In and Around San Francisco |
AM Hiking SF Coastal Trail to Land's End Beach with Bruce Conklin [attachment:LandsEndHike3.jpg trail map] http://www.josephstubbscreations.com/Home2/sf/sfparks/lincoln/lincoln.html |
|
AM Touring the historic Mission District murals with Allan Kuchinsky: http://www.precitaeyes.org/tours.html |
|
AM 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 Auditorium: 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
To be done
Location
To be done
Hotel Suggestions
To be done
Travel
To be done
Example Trip Planner
To be done
Amsterdam tourism
To be done