Cytoscape Wiki|
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'''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.''' |
'''This set of pages will from now on serve as the central site for the organization of the retreat. During the retreat this will also serve as starting point for notes, planning etc. The actual announcement site (now under construction) will come directly under the Cytoscape site; much like the tutorial pages are organized.''' |
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| 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] | The budget is stored as an excel sheet: attachment:CytoBudget.xls |
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| 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). | Planning is a separate wiki page''' CytoRetreat2007Planning ''' |
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| 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. |
---- = Discussion points for Cytoscape Board of Directors Teleconference, Wed 30th May 2007 = '''____''' |
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== Preliminary Schedule == ||<rowbgcolor="#ffeeaa">'''MON October 9th''' ||Gladstone Conference Rooms A & B || ||12:00PM-5:00PM ||["/Hackathon"] || ||5:30 PM ||tour of local campus, then dinner on own || ||<rowbgcolor="#ffeeaa">'''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 || ||<rowbgcolor="#ffeeaa">'''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) [[BR]]attachment: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"'' [[BR]]attachment: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"'' [[BR]]attachment:CytoscapeRetreat2006/Symposium/MiritAladjem_CytoscapeSymposium2006.ppt|| ||1:30PM-2:15PM ||[:CytoscapeRetreat2006/Symposium:Ilya Shmulevich] (ISB, Seattle)[[BR]]''"Data Integration and Genetic Network Modeling"'' [[BR]]attachment: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 || ||<rowbgcolor="#ffeeaa">'''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'' || ||<rowbgcolor="#ffeeaa">'''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 || ||<rowbgcolor="#ffeeaa">'''SAT October 14th''' ||In and Around San Francisco || ||NatureTour ||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 || ||UrbanTour ||AM Touring the historic Mission District murals with Allan Kuchinsky: http://www.precitaeyes.org/tours.html || ||AquaTour ||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/ [[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 Auditorium: attachment:Gladstone_Auditorium |
'''__Pre-Reading__: ''' |
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== 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]. |
Invitation Letters (Template) |
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| == Registration == | Sponsorship Requests (Template) |
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To be done ----- == Location == |
1st Announcement |
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To be done ----- == Hotel Suggestions == |
Budget Spreadsheet |
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To be done ----- == Travel == |
URL for the website (Test Site) |
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To be done ----- == Example Trip Planner == |
__'''Agenda''' __'''__Items__:''' |
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To be done ----- == Amsterdam tourism == |
1. __Web Site__ (Intention is to include this in all announcements) |
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| To be done |
1.1. URL: [http://www.cytoscape.org/Retreat2007 www.cytoscape.org/Retreat2007] 1.2. Test Site: http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007 1.3. Feedback on first impressions: navigation etc 2. __Retreat Programme__ - http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007/programme.php 2.1. Overview 2.2. Public Symposium . 2.2.1. Confirmed Speakers . 2.2.2. 2 Remaining Places: Proposed invitees are Andrew Hopkins - Pfizer, Ruedi Aebersold – ETH 2.3. Cytoscape Training Day . 2.3.1. Demand from users voiced in discussion forums 2.3.2. Tues 6th Nov, in parallel with Hackathon 2.3.3. Possibly Wed 7th, part of Demos 2.3.4. Trainers would not be developers (GW, Unilever bioinf team could do this) 2.4. Social Events - Several options dependent on number attending & weather 3. __Board & SAB Meeting __ 3.1. Options: Wed 18:00 PM or Thursday 18:00 PM 4. __Announcements __ 4.1. Will be made after web-site is stable 4.2. Which lists should we send announcements to? 4.3. 1st Announcement (see pre-reading material) 4.4. Subsequent Announcements: . 4.4.1. 2nd announcement for Registration opening (beginning July) 4.4.2. 3rd announcement after summer holidays (end of August) 5. __Budget Incomings__ 5.1. Cytoscape consortium contribution 5.2. Public Symposium Charges (assume max 400 pax) . 5.2.1. Should we charge fees for Public Symposium? 5.2.2. Academic / Non profit (50 euro) 5.2.3. Commercial, non sponsors (125 euro) 5.2.4. Allow opportunities for scholarship (to allow people to attend) 5.3. Sponsorship from Industry & Grant Bodies . 5.3.1. Sponsorship Requests (pre reading material) 5.3.2. Acknowledging sponsors (based on contribution) 5.3.3. Sponsorship so far (NBIC, Agilent, Unilever) 5.4. Accounting . 5.4.1. Which a/c to use (NL, US)? 5.4.2. Invoicing & Receipts 5.5. Other people / organisations / Universities to approach for sponsorship 6. __Budget – Outgoings__ 6.1. Spreadsheet 6.2. Assumptions underlying budget . 6.2.1. $10k from Cytoscape budget 6.2.2. 2 pax per institute 6.2.3. Economy flights 6.2.4. Funded developers share twin rooms 6.3. Who and what are we paying for? . 6.3.1. Speakers (flights, accommodation) 6.3.2. Developers (flights, accommodation) |
Cytoscape Retreat 2007
Amsterdam; the Netherlands - November 6th - 9th, 2007
This set of pages will from now on serve as the central site for the organization of the retreat. During the retreat this will also serve as starting point for notes, planning etc. The actual announcement site (now under construction) will come directly under the Cytoscape site; much like the tutorial pages are organized.
The budget is stored as an excel sheet: attachment:CytoBudget.xls
Planning is a separate wiki page CytoRetreat2007Planning
Discussion points for Cytoscape Board of Directors Teleconference, Wed 30th May 2007
Pre-Reading:
Invitation Letters (Template)
Sponsorship Requests (Template)
1st Announcement
Budget Spreadsheet
URL for the website (Test Site)
Agenda Items:
1. Web Site (Intention is to include this in all announcements)
1.1. URL: [http://www.cytoscape.org/Retreat2007 www.cytoscape.org/Retreat2007]
1.2. Test Site: http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007
1.3. Feedback on first impressions: navigation etc
2. Retreat Programme - http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007/programme.php
2.1. Overview
2.2. Public Symposium
- 2.2.1. Confirmed Speakers
- 2.2.2. 2 Remaining Places: Proposed invitees are Andrew Hopkins - Pfizer, Ruedi Aebersold – ETH
2.3. Cytoscape Training Day
- 2.3.1. Demand from users voiced in discussion forums 2.3.2. Tues 6th Nov, in parallel with Hackathon 2.3.3. Possibly Wed 7th, part of Demos 2.3.4. Trainers would not be developers (GW, Unilever bioinf team could do this)
2.4. Social Events - Several options dependent on number attending & weather
3. Board & SAB Meeting
3.1. Options: Wed 18:00 PM or Thursday 18:00 PM
4. Announcements
4.1. Will be made after web-site is stable
4.2. Which lists should we send announcements to?
4.3. 1st Announcement (see pre-reading material)
4.4. Subsequent Announcements:
- 4.4.1. 2nd announcement for Registration opening (beginning July) 4.4.2. 3rd announcement after summer holidays (end of August)
5. Budget Incomings
5.1. Cytoscape consortium contribution
5.2. Public Symposium Charges (assume max 400 pax)
- 5.2.1. Should we charge fees for Public Symposium? 5.2.2. Academic / Non profit (50 euro) 5.2.3. Commercial, non sponsors (125 euro) 5.2.4. Allow opportunities for scholarship (to allow people to attend)
5.3. Sponsorship from Industry & Grant Bodies
- 5.3.1. Sponsorship Requests (pre reading material) 5.3.2. Acknowledging sponsors (based on contribution) 5.3.3. Sponsorship so far (NBIC, Agilent, Unilever)
5.4. Accounting
- 5.4.1. Which a/c to use (NL, US)?
5.4.2. Invoicing & Receipts
5.5. Other people / organisations / Universities to approach for sponsorship
6. Budget – Outgoings
6.1. Spreadsheet
6.2. Assumptions underlying budget
- 6.2.1. $10k from Cytoscape budget 6.2.2. 2 pax per institute 6.2.3. Economy flights 6.2.4. Funded developers share twin rooms
6.3. Who and what are we paying for?
- 6.3.1. Speakers (flights, accommodation) 6.3.2. Developers (flights, accommodation)