SimBiology

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I have s SimBiology model in which the stochiometry of some equations depend on a model parameter called "DAR" as you can see below. I have DAR and some other paameters to change and see their effect on some observables. Once I change DAR and create a SimFunction, The stochiometry of equations do not change. Is there any way to use simFunction object and see the effect of DAR on the stchiometry. I can change the stochiometry in loop but I want it to be chnage as I use simFunction. Thanks reactionObj = addreaction(model,'Media.ADC_ext -> Media.Ab_ext + Media.PL_ext'); set (reactionObj, 'Stoichiometry', [-1 1 sbioselect(model,'Name','DAR').Value]) set (reactionObj, 'ReactionRate', 'kdec*Media.ADC_ext'); set (reactionObj, 'Notes', 'ADCs lose their payload, to produce unconjugated antibody and free payload'); set (reactionObj, 'Name', 'r1');

"Warning: Stoichiometry Math is not supported for species. The species 'ATP' in reaction 'MAS' will be read in with a stoichiometry of 1. "

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

While encoding a simple model of cell proliferation/death with rates r*X and d*X, which should result in an ODE such as dX/dt = r*X – d*X, I realised that it very much depends how the related 'Reaction' is formulated. With the correct stoichiometry 'B -> 2 B' all is fine but with 'B -> B' the growth flux is omitted entirely from the ODE. This is of course correct but it should come with a warning. I can imagin for complex model one is unable to verify whether the model is correctly interpreted and encoded. In this case the according reaction is visible in the diagram but the flux is not part of the relevant ODE. The question is: what are the other, if any, checks SimBiology performs behind the scenes which might result in differences between the model network and the model formulation?