Day 1 notes

Session 1: Cytoscape 2.6/2.7


Discussion threads:

Session 2: Cytoscape 3.0

Session 3: Cytoscape 3.0 (cont)

Session 4: Cytoscape 3.0 (cont)

Day 2 notes - planning

3.0 break out sessions

Layers for discussion


Refactor Group 1 Notes

Included: Scooter, Mike, John, Alex...

(to be filled in)

Refactor Group 2 Notes

Included: Allan, Gary, Ilya, Sarah, Benno...

Model Layer

Command Layer

This layer has some basic properties:

View Layer

This is not the presentation layer in that it contains no actual gui type presentation logic but is instead an abstract layer to handle all data associated (such as color mapping, coordinates, etc). Might help to rename this layer for clarity (ideas?). Few things that came up for the view layer to handle:

Application Layer

Plugin Developer Requests Group

These requests were gathered from plugin developers in a separate session on day 2. These are not necessarily comprehnsive and discussions should continue with plugin developers throughout the process.

Required functionality
  1. Graphics Access: In any refactored system access to raw drawing privatives (e.g. java 2D functions on the canvas) is required. This is for advanced graphics plugins.

  2. MDI operations: Control of position, and other layout properties for windows, through hints or similiar is desirable.

  3. Resource management: The use of a threading resource management system could be adopted. However, connection resource management is more specific to particular data sources and so was not felt to be practical.

Documentation and Specification
  1. Tutorials: Whilst documentation is important, tutorials and examples would also be required. The example plugins should not be of the “hello world” variety, but should consist of a hierarchy of the most common types of plugins (e.g. layout plugin example). These would, obviously, have to be maintained.

  2. Interfaces for plugin definitions: It was felt that, due to the multi faceted nature of plugins plugins, it would be difficult to describe just using a standard set of interfaces. Although in some cases such a role/functional description could be used.

  3. Development tools: Extensible plugin build and test files (through ant, maven or similar) is desired.

Other Issues

3.0 planning

Plans & Milestones

The following plans/milestones were agreed to at the end of the day on Friday. Mike Smoot will act as a coordinator and hand out tasks to the developers who signed up (listed below). All have agreed on the timeline and will continue to use the cytostaff list and wiki to help communicate.

Phase I

Milestone 1: Model Layer Specification. Due: End of January 2008

Milestone 2: Functional modular build with unit tests. Due: 2 month post 2.6 release (roughly end of March 2008)

Phase II (filled in further post PI/Milestone 1)

Milestone: Implementable model, working prototype Due: July 2008

Developer FTE's for 6 months






Mike, Kei, Peng






Scooter, Alex, Kristina










Hosp. for Sick Children



CytoscapeRetreat2007/HackathonNotes (last edited 2009-02-12 01:03:11 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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