1. Complete algorithm that use the CellDesigner Plugin API to calculate positioning for ReactionGlyphs and SpeciesReferenceGlyphs.
2. Establish way to synchronize CellDesigner's plugin datastructure and JSBML (so that CellDesigner models will be immediately and accurately represented in JSBML)
The first point has been completed. ReactionGlyphs and SpeciesReferenceGlyph positioning has been accurately implemented. I still have loose ends to tie up, but I am proud that my algorithms do the "right thing" in a variety of situations.
On the second point, I have created a plugin that receives events from CellDesigner and displays them in a console. As you can see, when the position of a species or reaction changes, CellDesigner informs the console.
The next step is to update the currently selected model in JSBML automatically when it is edited by the user.
I did run into problems in the plugin implementation and I had a few small hang-ups in regards to getting consistent reaction coordinates, but things are progressing very well :)