Wednesday, July 27, 2016

Week 13

Hello everyone,

This week I have been working on the reaction conversion from SBML Layout to CellDesigner annotation. Last week, I have completed converting reactions with 1 reactant and 1 product with 1 modifier.  For this week, I have completed converting reactions with multiple reactants/ products and with bezier curve.

While working on these conversions, I encountered two problems. First is defining bezier curve with one reactant and one product. Currently, I can only convert bezier curves only when there are multiple reactants and products like the second model above. I could not figure out a way to define a bezier curve in this situation. The second problem arises when the reaction contains the same species in both reactant and product. Every glyph is mapped to a unique SpeciesAnnotation. When working on the this kind of reaction both reactant and product were referencing the same species annotation. As a result, the output model would turn out as like the model below. To solve the second problem, I had to change up the main algorithm for conversion from SBML Layout to CellDesigner.

Model with same species as reactant and product

So, here is the chart for converting SBML Layout to CellDesigner Annotation. Blue means it's completed, red means it's not yet completed, green means it's unconvertable.

Since there is only 3 weeks left for GSoC, I have created a brief todo list.  Each tasks are ordered in priority levels, where the highest priority task coming up top. From now on, I will be mostly following this list.

No comments:

Post a Comment