MATLAB: Variable Stoichiometric Coefficients in SimBiology

Question

Hello,

I am trying to write down the following equation.

glucose -> a pyruvate

where a is some number between 0 and 2. Usually this is done for the conversion of sugar into some other chemical compound as e.g. pyruvate. The stoichiometrical relation however is usually not known because part of the glucose is converted into biomass. So for me "a" is a parameter and not a fixed number. I don't see a possibility to implement this in the reaction equations so far but I definitly need to estimate it later on.

Is there a solution to parametrize the stoichimetric coefficients of a reaction?

Thank you, Sebastian

Answer 1

Hi Arthur,

that is a great idea, and I am willing to try it out as soon as possible! I use varying compartment size with a repeated assignment so far, I will have to describe compartment size variation within the equations instead. How do I call the reactions rates for other reactions in this addrule assignment correctly ? They are readily present in the model object.

Thanks a lot Sebastian