MATLAB: Dosing in sbiofit example

dosingsbiofitSimBiology

Hi,

In the example "Fit a One-Compartment Model to an Individual's PK Profile" for the function sbiofit (the example is found in the sbiofit help page), an initial dose of 10 milligram is used:

dose = sbiodose('dose');

dose.TargetName = 'Drug_Central';

dose.StartTime = 0;

dose.Amount = 10;

dose.AmountUnits = 'milligram';

dose.TimeUnits = 'hour';

I just wonder where that value is coming from as it seems I cannot find it anywhere in the example. Should it be also a value that needs to be estimated, or it is a value that needs to be known from experimental/synthetic data?

Many thanks,

Jacopo

Best Answer

Hi Jacopo,

this is the dose amount used to generate the synthetic data used in this example.

But you are right, it should have been stated in the 'Background' section.

Another option to specify dosing is to include a dose column in the dataset. This gives you the flexibility to specify different dosing schedules and amounts for each group in your dataset.

There is an App-based example of this here.

You can see how doses are created from a dataset programmatically by generating MATLAB code from the Fit Program (it uses createDose() ):

Best regards,

Jérémy

Related Solutions

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);

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

Best Answer

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MATLAB: Do simfunctions support parameterized dosing

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

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