Organization team (so far)

Gary Bader
Chris Workman
Francis Ouellette

2008 retreat theme: community outreach - developers and users

The public Cytoscape Retreat 2008 page is at CytoscapeRetreat2008 This is the internal planning page.

Logistics

Retreat will be held July 16-19
Location: Toronto, CCBR building, University of Toronto
Main room: Red Room - capacity:~90 people (max 100 if needed)
Breakout room 1/lunch room: Black Room - capacity:~20 people + conference table

Schedule DRAFT

Technical session

July 15 (Tuesday)
- Pre-meeting core developer Cytoscape 3.0 design discussions (if necessary)
- Social event in evening for early arrivals (A)
July 16 (Wednesday)
- Audience: Mainly Cytoscape software developers
- Technical brainstorm, software design session
- Dinner event (B)

User session

July 17 (Thursday)
- Audience: All Cytoscape users and developers
- Application showcase day.
  - Developers will showcase interesting new features they are building for Cytoscape
  - Users will present interesting new uses of Cytoscape
- User community dinner (C)
July 18 (Friday)
- Audience: All Cytoscape users and developers
- User tutorial (morning parallel session)
- Developer tutorials (morning parallel session)
- User brainstorm and user meeting
  - Identify usability issues, request new features
  - Evolution game - problems people are having (gaps in workflows), find the common workflows and questions people want to ask.
  - Bring your data and speak to the experts.
  - Between plugin coordination issues: naming attributes, standards in event handling. Split people into groups - plugin writers vs. users. Goals: get plugins writers together to coordinate. Breakout session for plugin writers.
  - Scribes: assign roles
  - Wiki: expand each schedule item to its own page.
  - Book discussion: assign chapter leads
  - Cytoscape plugin developer users
  - Prepare materials in advance
  - Video recording of user tutorials. Adobe connect. Hire AV hire - find out how much that costs (Apple computer? Podcast producer?)
- Wine and cheese (D)
- Social event e.g. city tour, museum (E)
July 19 (Saturday)
- Audience: Users and developers interested in Cytoscape development
- Feature prioritization for Cytoscape 3.0.
  - Expect lots of technical discussion.
- Dinner on own (core developer dinner event) (F)

ISMB TODO

BOF: "bring your data" and speak to the experts. Plan agenda before.
Demo: Wodak, etc. (organize agenda at the retreat)

TODO

Add details to schedule (ongoing)
- Cytoscape 3.0 design discussions - intro sessions on specific technology.
- Application/plugin showcase day
- User/developer tutorial
Plan SAB meeting (Chris Workman)
Plan board meeting (Gary)
Submit demo and BOF request to ISMB organizers (done)
- BOF submitted: Network and pathway visualization and analysis, waiting for assigned day
Solicit showcase day presentations - enough material to create abstract book online
- As of Jun.19, almost 15 presentations have been submitted.
Plan Wed.July.23 morning ISMB session.
- TODO: send 100 words to Shoshana Wodak
- 2 hours
- People that will be around:
  - Piet Molenaar, Alex Pico, Gary Bader, Wodak lab, Scooter Morris
ISMB Conflicts:
- Scooter's tutorial is Saturday, July 19 morning
- BOSC July 18-19. Kei interested in presenting. http://www.open-bio.org/wiki/BOSC_2008
TODO: Find out how much money we have for travel fellowships and set up a committee for making decisions about that.

Agenda requests

Wednesday, July 16, technical session, agenda requests

Application showcase day presenter requests - July 17th

Barbara Mirel, UMich - afternoon, 10 minutes
Sarah Killcoyne, ISB
Allan Kuchinsky, Agilent - 5-10 minutes (cancelled)
David States - Michigan and NCIBI - 10 minutes
Scooter Morris, UCSF

Friday, July 18, user day

Cytoscape book discussion, afternoon (AllanK)

Saturday, July 19, prioritization day

Board meeting

New secretary/treasurer (Annette)
Cytoscape book - what's the goal? (Annette)

Attendees:

Trey
Gary
Annette
Alex (in lieu of Bruce)
Benno
Chris

Ilya
Bruce

Cytostaff Saturday dinner attendees: yes

Gary Bader
Allan Kuchinsky
Alex Pico
Trey Ideker
Piet Molenaar
Daniel Abel
Scooter Morris
Maital Ashkenazi
Chris Sander
Noel Ruddock
Yeyejide Adeleye

Mike Smoot (flying out at 7pm)
Sarah Killcoyne (flying out at 6pm)
Peng-Liang Wang

Survey results

31 respondents
Dates favored for the event:
- 73% July 16-19
- 30% July 23-26
- 20% July 19-22
Event content requests:
- 87% requested an application/plugin showcase day
- 74% user discussion sessions to identify and prioritize desired Cytoscape features
- 71% developer tutorials
- 58% social activities for community building
- 36% user tutorial part of ISMB
- 19% user tutorial not part of ISMB
Respondent comments:
- Prioritization after application showcase day;
- Discuss systems for profiling usage patterns and collecting user feedback;
- BOF discussion at ISMB in addition to retreat;
- One core developer discussion day not public;
- Formal usability studies;
- Usage showcase - more than a basic tutorial, presenting a complete workflow and not by plugin developers;
- cyto3.0 design discussions;
- Code sprints to focus development on needed areas;
- Would be nice if developer events were contiguous instead of being split around the application showcase