Differences between revisions 10 and 11

Mini-Retreat One

September 12-13, 2008
[http://www.ucsd.edu/maps/index.jsp?mapid=601&wid=601&iws=false&cat=&t=m&z=15&opacity=50&ll=32.88178563936398,-117.23437786102295 "Department of Bioengineering"] (Powell-Focht Bioengineering Hall), UC San Diego, Room 291
Mike's cell: 858-228-7242
Mike's office: 858-822-4756

Topics for Discussion

Progress on merging the new CyNetwork and CyAttributes model with the 3.0 branch.
- CyAttributes API changes based on retreat discussions (Trey's references [:CytoscapeRetreat2008/Design:notes]), CyDataTable
Discussion of how Groups will fit in to the model package.
Discussion of how HyperEdges will be handled.
Progress on ViewModel API?
Division of Labor - figure out what tasks can be separated out amongst other groups.

Get the application and at least one core plugin working with the new CyNetwork and CyAttribute models.

Gary opinion, Sep8 - Re: groups. Groups definitely belong in the model, but they should be kept separate from the core network model. There should be a CyGroups API similar to the one that exists that keeps track of all group information. Algorithms that work on simple graphs (most of the existing Cytoscape and plugin code) will not need to know about groups and those that need groups will be able to access the information using the CyGroups API. Group views on the other hand will likely need a lot of custom node shape functionality in the view layer. This is how Hyperedges should work as well.
Piet opinion, Sep9 - Re: goal. Isn't division of coding-labour one of the goals of these mini-retreats also?
Scooter, Sep 11 - I'm starting to get concerned that people might be spending too much time moving plugins over the Cy3 trunk without knowing how much the API is still in flux. We still haven't even talked about the View API much and a lot of plugins leverage various view features extensively. I think we should talk about exactly how people should be viewing Cy3 at this stage. We're going to have a lot of people really upset with us if they do a lot of work that has to be completely redone. On the other hand, we want people to give us input about what's missing in the tree, so some work is warranted.

Outdated_Cytoscape_3.0/MiniRetreatOne (last edited 2011-02-24 15:36:50 by PietMolenaar)

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+ * Scooter, Sep 11 - I'm starting to get concerned that people might be spending too much time moving plugins over the Cy3 trunk without knowing how much the API is still in flux.  We still haven't even talked about the View API much and a lot of plugins leverage various view features extensively.  I think we should talk about exactly how people should be viewing Cy3 at this stage.  We're going to have a lot of people really upset with us if they do a lot of work that has to be completely redone.  On the other hand, we want people to give us input about what's missing in the tree, so some work is warranted.