Outdated_Cytoscape_3.0/Mini_Retreat

• San Diego, June.17-18.2010
• Full day on the 17th starting at 9:30am and then a half day on the 18th

• Hotel: Sheraton La Jolla: http://www.starwoodhotels.com/sheraton/property/overview/index.html?propertyID=1959

• Focus: Cytoscape 3. What needs to be done for Cytoscape 3. Preparation for decision making at the Cytoscape retreat in July.
• Expected Attendees: Scooter Morris, Allan Kuchinsky, Samad Lotia, Sarah Killcoyne, Alex Pico, Mike Smoot, Keiichiro Ono, Peng-Liang Wang, Johannes Ruscheinski, Trey Ideker, Noel Ruddock (remotely), Gary Bader, Jason Montojo
• Resources:

  • Cytoscape_3.0

  • Cytoscape_3.0/DevelopmentModules

• Agenda
  • assumption that people have read all of the documents that Mike will send to cytostaff
  • overview of the documents to get everyone into the discussion

  • where we are with 3.0 - what is implemented. Brief overview of what needs to be implemented. With reference to Cytoscape_3.0/DevelopmentModules

  • architecture discussion - is osgi/spring/maven too difficult for people to learn. Will the OSGI barriers to adoption be overcome by maturation of the platform or is there something more fundamental? Should we have an abstraction layer to make it easier to write plugins for new plugin developers (Scooter will send a proposal about this). Core developers should be comfortable with the trade-off of complexity vs. ability to implement advanced architectural features. Notion of levels of integration of plugins - simplest to most complex plugins.
  • Desired outcome: commit to OSGI related architecture or not, once and for all

  • Review design issues. e.g. decide which modules should be refactored vs. rewritten e.g. CyAttributes. With reference to Cytoscape_3.0/DevelopmentModules

  • Goal: produce a fairly complete status report on the modules and decisions on how we are going to approach their design (keep like current implementation during 3.0 work or redesign)
  • Discussion about scoping 3.0 if time.

Discussion Note

• Cytoscape 3 Overview

  • 

• Agreements so far

  • 

• Startting point for 3

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Road Map

1. Cytoscape 3 Developer Preview
   • Strictly for developers
   • Minimal set of core modules including:

     • CyNetwork Model

     • Events

     • CyDataTables

     • View Model
   • Minimum requirements for the modules above:
     1. Complete set of public API separated from implementations
     2. All API should be fully documented
     3. Complete set of unit tests
2. Cytoscape 3 Alpha
3. Cytoscape 3 Beta
4. Cytoscape 3 RC
5. Cytoscape 3 General Release

Modules