MATLAB: Unable to see effect of “repeat dose” in simple Simbiology model

repeat doseSimBiology

Hi,

I'm trying to see the effect of a "repeat dose" block in a simple Simbiology model based on the "Create Model of Receptor-Ligand Kinetics" tutorial (see model attached). I added a "repeat dose" block to species L but it doesn't seem to work – I do not see the dose being added during the simulation. Can anyone tell me what I am doing wrong?

Thanks!

Jacopo

Best Answer

The issue was that the dosing was not active in the SimBiology Model Analyzer.

Related Solutions

MATLAB: Condition in which one compartment does not affect the mass balance

Hi Kazutaka,

In the example you are following along with (https://www.mathworks.com/help/simbio/ug/model-views.html), the PK part of the model is determined by a one compartment model with linear clearance (the compartment Central, with species Drug_Central and elimination reaction reaction_1). The biophase of the drug is modeled in a separate compartment: Biophase, with species Drug_Biophase, and creation reaction reaction_3 and elimination reaction reaction_2. The assumption in this model is that the drug concentration in the biophase does not affect the drug concentration in the central compartment and thereby the mass balance. This concept is implemented through reaction_3 : the stoichiometry of the reaction (Drug_Central -> Drug_Central + Drug_Biophase) has Drug_Central on both sides of the arrow, ensuring that Drug_Central is not being 'consumed' by the reaction. In other words: the concentration of Drug_Central is not affected by reaction_3 and reaction_3 doesn't show up in the ODEs for Drug_Central. In the diagram, this is illustrated by the dashed line between Drug_Central and reaction_3.

The assumption that the Biophase compartment does or doesn't affect the mass balance is a modeling decision made by the authors of the paper referenced at the bottom of the example page. As such, there is no condition that I can say your model should comply with in order to say that the compartment doesn't affect mass balance. The example merely states how to implement this.

I hope that helps. Let me know if you have further questions.

Best,

Sietse

MATLAB: Do simfunctions support parameterized dosing

Yes, parameterized doses are supported with SimFunctions. However, you cannot change the type of parameterization after creating a SimFunction. In your example, you created a SimFunction with a dose that was not parameterized, so you cannot simulate it with a parameterized dose table.

To create a SimFunction that uses a parameterized dose, replace your input {'drug'} with a "template" dose object that is parameterized. For example, you can re-use your existing dose for this by changing the next-to-last line of code to the following:

simFunction = createSimFunction(model,{},{'drug'},dose);

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Related Solutions

MATLAB: Condition in which one compartment does not affect the mass balance

MATLAB: Do simfunctions support parameterized dosing

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