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[[TableOfContents([2])]] <<TableOfContents([2])>>
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Lee Hood - Welcome Ilya Shmulevich - Notes from the Board attachment:Focus.ppt Lee Hood - Welcome Ilya Shmulevich - Notes from the Board [[attachment:Focus.ppt]]
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 * 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? attachment:DueDiligence.doc 		 * 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? [[attachment:DueDiligence.doc]]
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 * 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 attachment:UserExperience.doc 		 * 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 [[attachment:UserExperience.doc]]
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 * 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 		 * 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]]
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      * [http://isbsamples.googlecode.com/svn/trunk/ Sample code]
      * [http://www.martinfowler.com/articles/injection.html Martin Fowler article on dependency injection]
      * [http://www.eventhelix.com/RealtimeMantra/Object_Oriented/dependency_inversion_principle.htm Dependency inversion principle]
      * [http://www.osgi.org/osgi%5Ftechnology/ OSGi]
'''Discussion (for lead in to Friday)''' Review identified problems Discuss potential solutions attachment:DevPoints.doc 		      * [[http://isbsamples.googlecode.com/svn/trunk/|Sample code]]
      * [[http://www.martinfowler.com/articles/injection.html|Martin Fowler article on dependency injection]]
      * [[http://www.eventhelix.com/RealtimeMantra/Object_Oriented/dependency_inversion_principle.htm|Dependency inversion principle]]
      * [[http://www.osgi.org/osgi%5Ftechnology/|OSGi]]
'''Discussion (for lead in to Friday)''' Review identified problems Discuss potential solutions [[attachment:DevPoints.doc]]
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Mike Smoot attachment:Practicalities.doc Mike Smoot [[attachment:Practicalities.doc]]
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Break down the available RFCs into functional sets attachment:FunctionalSets.doc Break down the available RFCs into functional sets [[attachment:FunctionalSets.doc]]
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Match problems identified with RFCs Highlight problems which are not discussed in RFCs attachment:OrganizedProblems.doc Match problems identified with RFCs Highlight problems which are not discussed in RFCs [[attachment:OrganizedProblems.doc]]
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attachment:OrganizedFeatures.doc [[attachment:OrganizedFeatures.doc]]
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 * [:RFC_Template: New RFC Template] - Alex  * [[RFC_Template| New RFC Template]] - Alex
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Copy of the report sent to the board October 31, 2007: attachment:BoardReport20071031.pdf Copy of the report sent to the board October 31, 2007: [[attachment:BoardReport20071031.pdf]]

<<TableOfContents: execution failed [Argument "maxdepth" must be an integer value, not "[2]"] (see also the log)>>

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 Focus.ppt

Product Assessments

Powerpoint presentations for each package linked (except PathwayArchitect as requested):

Packages:

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? DueDiligence.doc

ISB User Experiences

  • Greg Carter – “issues with maintaining our plugins” & “issues with teaching Cytoscape” (Jen Smith, presented by Greg) CarterSlides.ppt

  • Ilya Shmulevich – “issues with use of Cytoscape by computational biologists” CompBioIssues.ppt

Discussion: Capture problems with Cytoscape Based on user experience and application discussions from the morning session UserExperience.doc

Discussion (for lead in to Friday) Review identified problems Discuss potential solutions DevPoints.doc

Practicalities of the Cytoscape Development Culture

Mike Smoot Practicalities.doc

Overview RFC’s

Break down the available RFCs into functional sets FunctionalSets.doc

Review the relevant RFCs and relate to identified problems

Match problems identified with RFCs Highlight problems which are not discussed in RFCs OrganizedProblems.doc

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

This document outlines the identified features to be worked on, organized into the same functional sets as the RFC's above. Note that items with a * are 3.0+ issues, any others should be considered in the 2.x series. OrganizedFeatures.doc

RFC's In Progress

These RFC's were identified as those most important to the "shopping list" for the board. Some of these may have RFC's already and may be added to or rewritten, others are new. A new RFC template will be used that will include a project plan for each with some idea of the time it will take and the project dependencies. Each of these will be used as the "shopping list" of ideas for re-architecting that will be presented to the board in November 2007.

New RFC’s:

  • New RFC Template - Alex

  • 3.0 RFC to reference all the … 3.0 RFC’s - Mike
  • Project – Scooter, Sarah
    • Server (low low priority)
  • Data mediator plugin (subgene viewer prototype) – Alex, Allan
  • Task Monitoring/Management - Scooter
  • Themes (see domain models: genomics, proteomics, etc) – Alex, Kei
    • “syntactic sugar”

Missing in Current RFC’s:

Plugin Refactor

  • API’s offered - Mike
  • Scripted plugins, proof of principle (just add a line, full RFC not required)
  • Plugin interoperability (OSGi) - Mike
  • Resource Management/Watcher – Mike (see API’s)
  • Test Framework - Mike

Relayering

  • Web front end, proof of principle for layering – Sarah, Allan*

  • Macros – Sarah (may be in the RFC already)
  • Consistent Event Handling – Sarah, Mike, Allan
  • What is associated with a node (Z,T, etc) – Sarah (discussion point)
  • Exception Handling - Sarah

*Allan: note that Web front end also has compelling use case of support for collaboration via sharing of networks and data. I can add a small description to this RFC.

Board Report

Copy of the report sent to the board October 31, 2007: BoardReport20071031.pdf

Oct2007SeattleMeeting (last edited 2009-02-12 01:04:12 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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