Hackathon discussion issues

Lessons learned in Cytoscape usability analysis

see ["Cytoscape usability studies"]
Suggestion: make this the first topic of the hackathon, as some of the points may be useful in the subsequent discussions.

Edge IDs should be addressable, just like node IDs
We should ensure that all of Cytoscape currently assumes directed edges - how/when do we deal with undirected edges?
GINY metanode refactoring: remove meta methods - all functionality will be present in the metanode/group API. This will significantly simplify the GINY API and data structure allowing developers to be more confident that their algorithms will work on CyNetwork in general.
Refactor the GINY interface/inheritance architecture: e.g. should we encapsulate GINY in CyNetwork? See ["CyNode Identification"]
Clean up depracated methods
More Unit tests for giny to help us make these changes
Clean up Cytoscape class – duplicated methods in CyNetwork vs. Cytoscape class and the general bloat of the Cytoscape class.

right now components that do mouse event and mouse motion event handling can clobber each other. Do we need an overall event architecture that components can plug into?
right now event declaration and listener store implementation is still spread out over a wide swath of the Cytoscape code. Should we consolidate into one event package?

how to accommodate arbitrary graphical annotations, such as text, legends, simple sketches, etc.
how to treat annotations that are attached to and move with nodes and edges, which can be handled by labels and custom graphics, from graphical annotations that are free standing
Ben's work on enhancing the InnerCanvas class to handle multiple layers, i.e. a NetworkCanvas, ForegroundCanvas, and BackgroundCanvas.
how to save and load graphical annotations.

When networks are destroyed, nodes, egdes and their attributes are not actually deleted, but maybe there should be some garbage collection if users want. Also, this allows attributes to pop back up for new nodes that are identically named to previously deleted nodes

What features should be in 3.0? There has been some brief discussion that the addition of metanode (group) and hyperedge concepts to the core (including some support for these in the UI) would qualify for 3.0 status.
How can plugins know which attributes are relevant to which network?
How should we deal with name clashes for cyattributes? Can we somehow detect name clashes and automate fixing these? Is this mainly a plugin issue?
Plan for reducing the number of libraries Cytoscape depends on e.g. refactoring to remove dependence on Piccolo