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

no

• 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

no

• 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