Cytoscape Wiki
Oct. 2007 Architecture Meeting - Seattle
Participants: Mike Smoot, John Boyle, Alex Pico, Allan Kuchinsky, Sarah Killcoyne, Scooter Morris, Ilya Shmulevich
Slides or documents that were presented have been uploaded as attachments throughout the agenda list.
Goal
To put together a “shopping list” of ideas to present to the board regarding re-architecting Cytoscape. To accomplish this we kept the discussion high level, avoiding discussion of code or specific releases directly as those details would continue to be handled by the core development group as a whole.
Agenda
Lee Hood - Welcome Ilya Shmulevich - Notes from the Board attachment:Focus.ppt
Product Assessments
Powerpoint presentations for each package linked (except PathwayArchitect as requested):
Packages:
Allan - PathwayArchitect
Mike - Biological Networks attachment:BiologicalNetworks.ppt
John - VisAnt attachment:VisAnt.ppt
- Scooter - Osprey attachment:Osprey.ppt
- Alex - Ingenuity attachment:Injenuity.ppt
Sarah - Pajek, CellDesigner attachment:Pajek.ppt attachment:CellDesigner.ppt
Discussion: Due diligence What do we like about these applications? Specifically look at the write-ups What have they done well, what might be useful to our users?
ISB User Experiences
Greg Carter – “issues with maintaining our plugins” & “issues with teaching Cytoscape” (Jen Smith, presented by Greg) attachment:CarterSlides.ppt
Ilya Shmulevich – “issues with use of Cytoscape by computational biologists” attachment:CompBioIssues.ppt
Discussion: Capture problems with Cytoscape Based on user experience and application discussions from the morning session
Related development experiences
Sarah Killcoyne – "integrating distributed ad-hoc data services" attachment:IntegratingData.ppt
John Boyle – "past experiences in managing the rearchitecting of mature products" attachment:MatureProducts.ppt
Hector Rovira – "software process used to refactor a plugin architecture into an existing commercial product" attachment:PluginArchitecture.pdf
Discussion (for lead in to Friday) Review identified problems Discuss potential solutions
Practicalities of the Cytoscape Development Culture
Mike Smoot attachment:Practicalities.doc
Overview RFC’s
Break down the available RFCs into functional sets attachment:FunctionalSets.doc
Review the relevant RFCs and relate to identified problems
Match problems identified on Thursday with RFCs Highlight problems which are not discussed in RFCs
Planning based on problems and grouped RFC’s
Present high level ideas for solving the problems: including strategies for implementation, preliminary timelines, problems and dependencies Establish groups to work on adapting old (or producing new) RFCs Put together “shopping list” of ideas to present to board