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| 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. | 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. |
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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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* 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 |
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'''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 |
* 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? 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 '''Discussion (for lead in to Friday)''' Review identified problems Discuss potential solutions attachment:DevPoints.doc |
* 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 attachment:DevPoints.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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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 |
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 |
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| 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. | 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. |
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* 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” |
* 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” |
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* 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 |
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* 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 |
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* Web front end, proof of principle for layering – Sarah * 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 |
* Web front end, proof of principle for layering – Sarah'', Allan'' ''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.'' * 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 |
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? attachment:DueDiligence.doc
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 attachment:UserExperience.doc
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 attachment:DevPoints.doc
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 with RFCs Highlight problems which are not discussed in RFCs attachment: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
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
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.
- 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