Hackathon discussion issues

GINY Refactoring

• 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.

VizMapper/Filtering redesign

• see ["VizMapUI"]

Technology sharing with InfoVis Toolkit

• see ["InfoVis Toolkit"]

Integration of Hyperedges and Metanodes APIs into the core

• Hyperedges
• Metanodes

Graph Layout Architecture

Event handling

Uncategorized

• 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?