Tuesday, May 17, 2016

Week 3

Hello everyone,

sorry for not posting last week. I have been a bit busy with other stuff.

So far I have done the following.
  • Downloaded JSBML maven project 
  • Created sample program to try out the API for the layout
  • Read GSoC 2014 project code by Ibrahim Vazirabad and his blog

As the first step of my project, I must figure out a way to create an API for CellDesigner annotation in a SBML file.  Since it will be a standalone software,  the software can not use the CellDesigner as Ibrahim did.  After this has been resolved,  I will be working on to convert the CellDesigner annotation to pure SBML with layout extension.

In Ibrahim's project,  he mentioned how CellDesigner classes are mapped to that of SBML. I thought it will be useful so I will post it here for future reference.

Also to check if my conversion is correct, the SBML Layout Viewer by Dr. Frank Bergmann may be come in handy.

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