Cytoscape Wiki|
Size: 6949
Comment:
|
Size: 3773
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| '''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.''' |
| Line 6: | Line 6: |
| 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:CytoBudget2007.xls |
| Line 8: | Line 8: |
| Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Examples of features added in this way are network and molecular profiling analyses, new layouts, additional file format support and connection with external databases. Cytoscape is written in Java and the code is completely open source. The software architecture enables adaptation of Cytoscape functionality to the specific needs of molecular biologists and bioinformaticians. This is obvious from the range of research groups in a wide variety of fields that use Cytoscape to facilitate publications in high-profile scientific journals (See figure 1 for some examples). | A preliminary compilation of potential maillists to send announcements to is stored as an excel sheet: attachment:Potential_Maillists.xls |
| Line 10: | Line 10: |
| 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). These groups have dedicated themselves to maintaining and further developing Cytoscape and providing support to the user community. | Planning is a separate wiki page:''' CytoRetreat2007Planning ''' |
| Line 12: | Line 12: |
| The Cytoscape community organizes a retreat each year to establish a roadmap for Cytoscape development. Until now these were held in the USA. At last year’s retreat the possibility of organizing the next retreat in Europe was raised and the Cytoscape team was enthusiastic. The Human Genetics Department of the AMC has accepted the challenge of organizing the meeting. |
---- = Discussion points for Cytoscape Board of Directors Teleconference, Wed 30th May 2007 = '''____''' |
| Line 14: | Line 16: |
| The goal of the retreat is threefold: | '''____''' |
| Line 16: | Line 18: |
|
. 1: Involve the large user community in Europe in Cytoscape development; create a Cytoscape bridgehead in the Netherlands . 2: Gather user feedback and use it to plan future development. . 3: Establish a development roadmap for the next year |
== Pre-Reading: == . Invitation Letters (Template) . Sponsorship Requests (Template) . 1st Announcement == Agenda Items: == General Planning: CytoRetreat2007Planning |
| Line 20: | Line 25: |
| We want to reach these goals in a retreat spanning four days. The first and last day are mainly intended for the Cytoscape core development team and other developers who write their own Cytoscape plugins. The second and third days are aimed at a wide audience of molecular biologists and bioinformaticians in the Netherlands, Europe and internationally and to attract them we will invite several high profile speakers. | 1. __'''Web Site'''__ (Intention is to include this in all announcements) |
| Line 22: | Line 27: |
| The meeting will be partly 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. |
. 1.1. URL: www.cytoscape.org/Retreat2007 . 1.2. Test Site: http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007 . 1.3. Feedback on first impressions (navigation, design, etc) would be appreciated 2. __'''Retreat Programme'''__ - http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007/programme.php |
| Line 24: | Line 32: |
| On the other hand the public symposium will offer an excellent scientific program capable of attracting participants independently of the rest of the retreat activities. | 2.1. Run rogramme overview (please see link above) |
| Line 26: | Line 34: |
|
== Preliminary Schedule == ||<rowbgcolor="#ffeeaa">'''MON November 5th''' ||'''Meet and greet''' || ||<rowbgcolor="#ffcc99">'''Where''' ||Somewhere in Amsterdam || ||5:00PM-7:00PM ||Meet and greet in bar || ||7:00 PM-(...) ||Dinner on own but together ;-) || ||<rowbgcolor="#ffeeaa">'''TUE November 6th''' ||'''Hackathon''' || ||<rowbgcolor="#ffcc99">'''Where''' ||AMC Lectureroom K 01-123 || ||9:30-11:00 ||Defining issues and breakout groups || ||11:00-11:30 ||Coffee break || ||11:30-12:30 ||Hacking/Coding in breakout groups || ||12:30-14:00 ||Lunch || ||14:00-15:30 ||Hacking/Coding in breakout groups || ||15:30-16:00 ||Coffee and tea break || ||16:00-17:00 ||Results session || ||17:00-(...) ||Hackathon Extension; things todo in Amsterdam || ||<rowbgcolor="#ffeeaa">'''WED November 7th''' ||'''Demoday''' ''Application showcase and hands-on sessions'' || ||<rowbgcolor="#ffcc99">'''Where''' ||AMC Lecturerooms K 01-123 and -122 ; parallel sessions || ||9:30-11:00 ||Application showcase 1A / Hands-on session 1A || ||11:00-11:30 ||Coffee break || ||11:30-12:30 ||Application showcase 1B / Hands-on session 1B || ||12:30-14:00 ||Lunch || ||14:00-15:30 ||Hands-on session 2A/Application showcase 2A || ||15:30-16:00 ||Coffee and tea break || ||16:00-17:00 ||Hands-on session 2B/Application showcase 2B || ||17:00-(...) ||Hackathon Extension; things todo in Amsterdam || ||18:00-(...) ||SAB & Board of Directors Meeting || ||<rowbgcolor="#ffeeaa">'''THU November 8th''' ||'''Public Symposium''' ''Cytoscape: Network-Based Approaches to Biological Data Integration and Analysis'' || ||<rowbgcolor="#ffcc99">'''Where''' ||AMC Conference Room 5 || ||9:15-9:30 ||Opening || ||9:30-10:15 ||Speaker 1 || ||10:15-11:00 ||Speaker 2 || ||11:00-11:30 ||Coffee break || ||11:30-12:00 ||Speaker 3 || ||12:00-12:30 ||Speaker 4 || ||12:30-14:00 ||Lunch || ||14:00-14:45 ||Speaker 5 || ||14:45-15:30 ||Speaker 6 || ||15:30-16:00 ||Coffee and tea break || ||16:00-16:30 ||Speaker 7 || ||16:30-17:00 ||Speaker 8 || ||19:00-(...) ||Conference Dinner || ||<rowbgcolor="#ffeeaa">'''FRI November 9th''' ||'''Roadmap''' ''Defined by devteam'' || ||<rowbgcolor="#ffcc99">'''Where''' ||AMC Lecturerooms K 01-123 || ||9:30 || Cytoscape 2.5 rundown || ||10:30 || Organize Major Development Tasks and BreakoutGroups07 || ||12:30 || Working Lunch || ||13:00 || BreakoutGroups07 Report || ||13:00 || Parallel session of Board of Directors and SAB to discuss vision || ||15:00 ||Work on RoadMap2007 / Match Core Developers to Action Items || ||17:00 ||Wrap-up: SAB Input, Board Issues & Future Vision || ||18:45-(...) ||Things todo in Amsterdam || == Registration == To be done |
2.2. Public Symposium |
| Line 80: | Line 36: |
|
----- == Location == To be done |
. 2.2.1. Confirmed Speakers: * Lee * Trey * Benno * Chris * Peter Sorger * Ewan Birney . 2.2.2. Two Remaining Places: Proposed invitees are * Andrew Hopkins - Pfizer * Ruedi Aebersold – ETH * Jean-Daniel Fekete - Institut Pasteur 2.3. Cytoscape Training Day |
| Line 84: | Line 49: |
|
----- == Hotel Suggestions == To be done |
. 2.3.1. Demand from users voiced in discussion forums . 2.3.2. Could take place Tues 6th Nov, in parallel with Hackathon . 2.3.3. Trainers would not be developers (GW, Unilever bioinf team could do this) 2.4. Social Events - Several options dependent on numbers attending & weather |
| Line 88: | Line 54: |
|
----- == Travel == To be done |
3. __'''Board & SAB Meeting''' __ |
| Line 92: | Line 56: |
|
----- == Example Trip Planner == To be done |
3.1. Options: Wed 18:00 PM or Thursday 18:00 PM - What do people prefer? |
| Line 96: | Line 58: |
|
----- == Amsterdam tourism == To be done |
4. __'''Announcements''' __ 4.1. Will be made after web-site is stable 4.2. Which mailing lists should announcements be sent to? 4.3. 1st Announcement (please 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'''__ attachment:CytoBudget2007.xls 5.1. Cytoscape consortium contribution 5.2. Public Symposium Charges (assume max 400 participants) . 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 (please see pre reading material) . 5.3.2. Acknowledging sponsors (Order of appearance 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. Suggestions for other people / organisations / Universities to approach for sponsorship? 6. __'''Budget – Outgoings'''__ attachment:CytoBudget2007.xls 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:CytoBudget2007.xls
A preliminary compilation of potential maillists to send announcements to is stored as an excel sheet: attachment:Potential_Maillists.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
Agenda Items:
General Planning: CytoRetreat2007Planning
1. Web Site (Intention is to include this in all announcements)
- 1.1. URL: www.cytoscape.org/Retreat2007
1.2. Test Site: http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007
- 1.3. Feedback on first impressions (navigation, design, etc) would be appreciated
2. Retreat Programme - http://humangenetics-amc.nl/test/CytoWebRedux/retreat2007/programme.php
2.1. Run rogramme overview (please see link above)
2.2. Public Symposium
- 2.2.1. Confirmed Speakers:
- Lee
- Trey
- Benno
- Chris
- Peter Sorger
- Ewan Birney
- 2.2.2. Two Remaining Places: Proposed invitees are
- Andrew Hopkins - Pfizer
- Ruedi Aebersold – ETH
- Jean-Daniel Fekete - Institut Pasteur
2.3. Cytoscape Training Day
- 2.3.1. Demand from users voiced in discussion forums
- 2.3.2. Could take place Tues 6th Nov, in parallel with Hackathon
- 2.3.3. Trainers would not be developers (GW, Unilever bioinf team could do this)
2.4. Social Events - Several options dependent on numbers attending & weather
3. Board & SAB Meeting
3.1. Options: Wed 18:00 PM or Thursday 18:00 PM - What do people prefer?
4. Announcements
4.1. Will be made after web-site is stable
4.2. Which mailing lists should announcements be sent to?
4.3. 1st Announcement (please 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 attachment:CytoBudget2007.xls
5.1. Cytoscape consortium contribution
5.2. Public Symposium Charges (assume max 400 participants)
- 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 (please see pre reading material)
- 5.3.2. Acknowledging sponsors (Order of appearance 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. Suggestions for other people / organisations / Universities to approach for sponsorship?
6. Budget – Outgoings attachment:CytoBudget2007.xls
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)