Wednesday, August 17, 2016

Final week (week 16)

Hi all,

Only few more days are left until I submit my work. And last week, I left off with some unfinished tasks. Here are the todo list from last week. Darker blue means for the conversion from SBML Layout to CellDesigner Annotation and lighter blue means  for the conversion from CellDesigner Annotation to SBML Layout.

For this week, I have mainly worked on 1st, 3rd, and 4th tasks. As for the conversion of bezier curve,  I have converted the bezier curve into line segments, since CellDesigner does not allow a bezier curve with the reaction with one reactant and one product.

Bezier original

Bezier converted

For the 3rd task, I have added conversion for reaction with modifiers with branches.

Modifier with branches original

Modifier with branches converted

Also, for the 4th task, adjusting the arrowhead, I have moved the end point of the line segment to go to the boundary of the glyph.

arrowhead before

arrowhead after

Additionally, I have fixed the conversion for FBC package. I have added the conversion for reaction with boolean logic operators.

boolean model

boolean model converted 

So for the next few days, I have to work on the 2nd task and wrap up the project.

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