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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.


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.


Lee Hood - Welcome Ilya Shmulevich - Notes from the Board Focus.ppt

Product Assessments

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


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

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:

Missing in Current RFC’s:

Plugin Refactor


*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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