Cytoscape WikiGaryBader - Dec.14.2005 - Re: question 1 - It seems that if the API supports programmer extensibility of event handling and semantics in a clear and UI-independent way, that UIs could be built to support user extensibility of these later - even as plugins. For instance, the CytoPanel API would allow someone to write a plugin that created a control center for CytoPanels, that allows all tabs to be opened/closed, rearranged, etc.
Re: Question 6 - you don't need a BioPAX exporter to go with the BioPAX editor because all state could be saved as Cytoscape attributes and loaded back in. It would be very useful to have a BioPAX exporter, however, which maps from predefined attributes to fields in BioPAX.