MATLAB: Applying Variants in Simbiology for Different Datasets during Parameter Estimation

parameter estimationpk modelSimBiologyvariants

I have seen some similar questions about this but they haven't quite answered what I need to do.

For my set-up I have a simple compartmental model which describes drug distribution, the volumes of these compartments is dependent on a parameter ( Bodyweight)

I am trying to parameterise the model using several datasets which are pooled to provide a single parameter set

However each dataset comes from a different experiment where the bodyweights are different and so I cannot use a single set bodyweight for all as it bias' my parameter estimations

Does anyone know how I could set a parameter estimation so that for each dataset a different value for the parameter Bodyweight is used?

Best Answer

Today, you cannot directly apply group-specific variants during fitting. (But this is definitely on our radar as something customers want to do.)

It's not terribly straightforward, but one workaround is to create "fake" group-specific dosing that sets the bodyweight for each group. I describe this sort of approach in more detail in this post.

If you still have questions, post a reply. But if you don't hear back in a timely fashion, you can contact me directly through my user profile. (I don't get notified when you reply to my answer.)

-Arthur

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MATLAB: Sbiofit example – Fit a One-Compartment Model to an Individual’s PK Profile using SimBiology app

Hi Jacopo,

I have had a look at your project. There were two things which differed from the programmatic example:

you set the response to be a measurement of Dose_Central whereas it should have been Drug_Central
unit conversion was not turned on. That being said, it would not prevent you from getting the right results because the model and dataset are in the same units.

I have attached your project with these modifications.

Let me now answer your questions:

Why is ka_Central not estimated in this case? Shouldn't it be estimated as it is part of the one-compartment model used here?

ka_Central is not estimated because we only have IV data in this example. The dose is given to Drug_Central and we measure Drug_Central. So, we wouldn't have any information in this dataset to estimate ka_Central.

What happens if a dose has different units? E.g. gram instead of milligram for this particular example? Does SimBiology automatically detect the different units and convert them appropriately?

SimBiology can deal with different units as long as they are all using amounts or all using mass. For this, you need to activate unit conversion by clicking on this button in the Model Tab of the SimBiology App:

Best regards,

Jérémy

MATLAB: Accessing a variant object

Hi Deepa,

you can access the variant content with the dot notation.

If your variant is called v, v.Content will be an array of cell array with one row per component in this variant.

That being said, I like to convert variants into a table to handle it. For this you can use the following function:

function tableObj = sbiovariant2table(variantObj)
% tableObj = sbiovariant2table(variantObj)
%
% Converts the content of a variant to a Table that can be exported to
% Excel with writeTable
content = vertcat(variantObj.Content{:});
tableObj = cell2table(content,'VariableNames',{'Type','Name','Property','Value'});
tableObj.Name = string(tableObj.Name);
tableObj.Type = categorical(tableObj.Type);
tableObj.Property = categorical(tableObj.Property);
tableObj.Properties.Description = variantObj.Name;
end

With this function you can retrieve all species easily:

tableVar = sbiovariant2table(v);
speciesInVar = tableVar(tableVar.Type == 'species',{'Name','Value'})

Best Answer

Related Solutions

MATLAB: Sbiofit example – Fit a One-Compartment Model to an Individual’s PK Profile using SimBiology app

MATLAB: Accessing a variant object

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