Differences between revisions 8 and 35 (spanning 27 versions)

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

Program for Cytoretreat organization meeting

Amsterdam, Tue 31st July - Wed 1st August 2007

Tue 31st July
Time	What	Where	Who
12:00	Collect Annette	Central Station	Annette, Piet
13:00	Visit VU	Subway stop VU-Boelelaan(include maplink)	Annette
16:00	Visit AMC	Subway stop AMC-Holendrecht	Annette, Piet
20:00	Take it easy	Amsterdam	Annette, Piet
22:00	Collect Guy	Central Station	Annette, Guy, Piet
22:15	Supper: discuss probable events for social program(Piet: Attach agenda,docs)	Probable Conf.dinner location(Piet: add link)	Annette, Piet, Guy
24:00	Drinks: discuss probable events for social program	Probable Conf drinks location(Piet: add link)	Annette, Piet, Guy

Wed 1st August
Time	What	Where	Who
9:00	Leave for AMC	Respective places	A,P,G
9:15	Visit venue; rooms etc	Subway stop AMC-Holendrecht	A,P,G
11:00	Discuss program: create todo list: setup demoday(Piet: Attach agenda,docs)	AMC	A,P,G
13:00	Lunch	Amsterdam center	A,P,G
14:30	Visit probable places to stay; social events locations	Amsterdam center:	A,P,G
20:00	Dinner	Probable Conf.dinner location	A,P,G
22:00?	Leave	Central Station	Annette, Guy

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
- [http://www.lri.fr/~fekete/ Jean-Daniel Fekete] - INRIA France

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)

-  ← Revision 8 as of 2007-02-21 12:29:28 →
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+  ← Revision 35 as of 2007-07-19 14:25:13 →
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-Deletions are marked like this.
+Additions are marked like this.
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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.'''
 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:
-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:
-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), Annette Adler (Agilent Technologies, Santa Clara, CA) 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:
-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.
+----

== Program for Cytoretreat organization meeting ==

=== Amsterdam, Tue 31st July - Wed 1st August 2007 ===
-Line 14:
+Line 16:
-The goal of the retreat is threefold:
+||||||||<style="text-align: center;">'''Tue 31st July''' ||

||'''Time''' ||'''What''' ||'''Where''' ||'''Who''' ||

||12:00||Collect Annette||Central Station ||Annette, Piet||

||13:00||Visit VU ||Subway stop VU-Boelelaan(include maplink) ||Annette||

||16:00||Visit AMC||Subway stop AMC-Holendrecht ||Annette, Piet||

||20:00||Take it easy ||Amsterdam ||Annette, Piet||

||22:00||Collect Guy||Central Station ||Annette, Guy, Piet||

||22:15||Supper: discuss probable events for social program(Piet: Attach agenda,docs)||Probable Conf.dinner location(Piet: add link) ||Annette, Piet, Guy||

||24:00||Drinks: discuss probable events for social program||Probable Conf drinks location(Piet: add link) ||Annette, Piet, Guy||

'''____'''

||||||||<style="text-align: center;">'''Wed 1st August''' ||

||'''Time''' ||'''What''' ||'''Where''' ||'''Who''' ||

||9:00||Leave for AMC||Respective places ||A,P,G||

||9:15||Visit venue; rooms etc||Subway stop AMC-Holendrecht ||A,P,G||

||11:00||Discuss program: create todo list: setup demoday(Piet: Attach agenda,docs)||AMC ||A,P,G||

||13:00||Lunch||Amsterdam center||A,P,G||

||14:30||Visit probable places to stay; social events locations||Amsterdam center: ||A,P,G||

||20:00||Dinner||Probable Conf.dinner location ||A,P,G||

||22:00?||Leave||Central Station||Annette, Guy||
-Line 16:
+Line 36:
- . 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
+----
-Line 20:
+Line 38:
-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.
+== Discussion points for Cytoscape Board of Directors Teleconference, Wed 30th May 2007 ==

'''____'''
-Line 22:
+Line 41:
-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.
+'''____'''
-Line 24:
+Line 43:
-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.
+=== Pre-Reading: ===

 . Invitation Letters (Template)

 . Sponsorship Requests (Template)

 . 1st Announcement

== Agenda Items: ==

General Planning: CytoRetreat2007Planning
-Line 26:
+Line 50:
-== 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
+. __'''Web Site'''__ (Intention is to include this in all announcements)
-Line 80:
+Line 52:
------

== Location ==

To be done
+ . 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 84:
+Line 57:
------

== Hotel Suggestions ==

To be done
+.1. Run rogramme overview (please see link above)
-Line 88:
+Line 59:
------

== Travel ==

To be done
+.2. Public Symposium
-Line 92:
+Line 61:
------

== Example Trip Planner ==

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

  * [http://www.lri.fr/~fekete/ Jean-Daniel Fekete] - INRIA France

2.3. Cytoscape Training Day
-Line 96:
+Line 74:
------

== Amsterdam tourism ==

 * [http://www.waterlelie-rondvaart.nl/ Roundtrip by boat]
+ . 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)