Tuesday, August 5, 2014

The Final Week is here!

Hello all,

I have quite a bit to report on the advancement of my project.

My current checklist was as so:

1. Complete synchronization of CellDesigner plugin model and JSBML.
2. maintain map of SBases.
2. Finish Render Extension additions
3. Work on adding cases to Reaction positioning algorithm(main reaction axes over 4 points were never handled, very diverse minority of cases)

During the last meeting, it was found that Rules, UnitDefinition, Events, Constraints, Parameters, etc are not synchronized in CellDesigner. Also, it was also found that IDs for many CellDesigner PluginSBases can be changed, and are not constant. Therefore, we could not depend on Ids to synchronize the CellDesigner and JSBML models.

As such, a new algorithm was proposed for Changing and Deleting SBases.

If a PluginSBase(other than Models or Compartments) is changed or deleted, we:
1. delete all associated JSBML objects in Model and Layout
2. delete them from the Map of SBases
2. re-add them directly from the CellDesigner model.

This has been done for all CellDesigner PluginSBases, and as such, there is a thorough synchronization.
The map is also maintained properly.

On the Layout front, I FINALLY got reaction axes over 4 points to be read properly by my algorithm. There are still small bugs that need to be fleshed out, but I am happy a few downloaded models actually render 95%+ properly.

The above model did not render properly until main reaction axes over four points were handled. This is an excellent way to assure conformance to models "in the wild".

Adding render information has always been difficult due to the complexity of the Render Extension itself, so I have not been getting very far on that. But I hope tomorrow will be a better day for that.

Finally, my practice presentation for the final presentation is going to be on the 13th in preparation for COMBINE on the 20th. I will need to start creating some demos to show off the progress I have made this summer on improving the JSBML/CellDesigner plugin interface.

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