Tuesday, May 31, 2016

CellDesigner → SBML

Hello all,

Last week, I have created APIs from schemas.  Using the APIs, I have tested if I can get the attributes from XML. With the test, I have figured out that I could not obtain the celldesigner:reactionType attributes (already fixed).

For the past week,  I have been implementing the converter that converts CellDesigner annotation to SBML Layout. The brief outline of the converter is as follow.

  1. Read XML using the generated APIs
  2. Read XML using JSBML
  3. Copy datas from 1. to the wrappers which were implemented last week
  4. From 3. copy the necessary datas into 2. 
So far, I have implemented conversion of compartment and speciesAlias. Figures shown below are the original model created with CellDesigner and the output model visualized with SBML Layout Viewer. As you can see, most diagrams are in the same layout. However the text for each diagram still needs some adjustments. 

For next week, I will be implementing the conversion of reactions (the lines show in the diagram). And I am hoping to  start the conversion from SBML layout to CellDesigner.

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