Monday, July 28, 2014

Synchronizing CellDesigner and JSBML, Contact with Akira and Checklist

Just a quick update since it is late here, but over the past week, I have been continuing with my synchronization of the JSBML/CellDesigner(CD) model representations. I have added a Map<PluginSBase, Set<SBase>>. The key is the CD object and all JSBML objects associated with the CD object.

Since establishing contact with the main developer of CellDesigner (Dr. Akira Funahashi), I have sent him an email detailing some questions I had regarding CellDesigner.

My questions to him:

1.  Is there is an accurate way to determine the reaction direction, be it North-South, East-West, etc? This answer will be very useful in determining the position of the Reaction text element, as it is calculated dynamically behind the scenes in CellDesigner.

2.According to the image below, when the CD user moves only a Reaction, nothing happens. One has to move a Species to send a Reaction SBaseChange event. This is unexpected and I would like some clarification on this if possible.

3. Some CellDesigner model files force CellDesigner to send SBaseChanged events every time one part of the model is changed. This is odd behavior, as if the whole model is changed when one small part is changed. It is even more odd considering as other models only send SBaseChanged events for PluginSBases that are edited by the user rather than an event for every PluginSBase in the model. 

Current checklist for myself:

1. Add Render information
2. setCharge()/ FBC. 
3. add reactiontext info, fix bugs
4. find species reference sbases in CellDesigner

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