Simulate different dosing amounts with a schedule dose

Does anybody know if there is a way to perform a parameter scan of a dose amount if the dose object is a schedule dose? Or do I need to create one dose object manually for each dose level that I want to simulate.

Thanks,

Answer 1

[Florian Augustin]

Hello,

parameterized schedule doses are currently not supported (Matlab release R2021b), only repeat doses can be parameterized. As you already mentioned, in order to scan over schedule doses you have to create separate dose objects. Here is an example how you could do it on the MATLAB command line:

% Load example model

modelObj = sbmlimport("radiodecay.xml");

% Define dose amounts to scan over

doseAmountValues = [50, 100, 200];

numAmountValues = numel(doseAmountValues);

% Schedule times

scheduleTimes = [1, 2, 3, 4];

% Create schedule doses

for idx = 1:numAmountValues

scheduleDoses(idx) = sbiodose("dose amount " + doseAmountValues(idx), "schedule"); %#ok<*SAGROW>

scheduleDoses(idx).TargetName = "x";

scheduleDoses(idx).Time = scheduleTimes;

% Here the same dose amount is applied at every scheduled time,

% but the actual dose schedule and parameterization may be more complex.

scheduleDoses(idx).Amount = [1, 1, 1, 1] * doseAmountValues(idx);

end

% Create scenarios to scan over the doses

scenarios = SimBiology.Scenarios("doses to scan over", scheduleDoses);

% Create a simulation function for the model

simFun = createSimFunction(modelObj, scenarios, "x", [], "AutoAccelerate", false);

% Simulate the model for every dosing scenario

simData = simFun(scenarios, 10);

% Plot the results

sbioplot(simData);

Here is a list of references to the documentation that may be helpful

• SimBiology scenarios
• Create and simulate a model using SimFunctions

If your schedule doses are regular enough, you could use repeat doses instead; but I assume this is not the case in your application? If this was the case, you could just create one repeat dose, parameterize the Amount property, and then scan over the parameter used for the parameterization of the amount. For repeat doses, you could also use a "Run Scan" program in the SimBiology Model Analyzer app to perform the parameter scan over different dose amounts.

-Florian

[Zinnia Parra-Guillen]

I am dosing at days 1,3,5,8 and then every 21 days, but I do not think I can create 5 dose objects and update them simultaneously for the parameter scan, right?

Thanks a lot for the code!

Zinnia

[Florian Augustin]

Hi Zinnia,

You are right, that will work. It sounds like you may even only need two repeat doses. One for the initial treatment (days 1, 3, 5) and one for the continued treatment (days 8, 29, 50, ...). Here is an example for how you could implement this on the command line:

% Load example model

modelObj = sbmlimport("radiodecay.xml");

% Define dose amounts to scan over

doseAmountValues = [50, 100, 200];

% Add dose parameter to the model

addparameter(modelObj, "doseAmount");

% Create repeat doses

initialTreatment = sbiodose("dose days 1, 2, 3", "repeat");

initialTreatment.TargetName = "x";

initialTreatment.Amount = "doseAmount"; % parameterized amount to scan over

initialTreatment.StartTime = 1; % first dose on day one

initialTreatment.RepeatCount = 2; % repeat application of this dose twice

initialTreatment.Interval = 2; % 2 day interval

continuedTreatment = sbiodose("dose every 21 days", "repeat");

continuedTreatment.TargetName = "x";

continuedTreatment.Amount = "doseAmount"; % parameterized amount to scan over

continuedTreatment.StartTime = 8; % first dose on day eight

continuedTreatment.RepeatCount = 10; % repeat application of this dose ten times

continuedTreatment.Interval = 21; % repeat dose every 21 days

% Create scenarios to scan over the doses;

% this creates scan scenarios for you where the two doses are applied for every

% value (in doseAmountValues) you want to scan over.

% Create scenarios to scan over the doses

doseScenarios = SimBiology.Scenarios("initial treatment", initialTreatment);

add(doseScenarios, "elementwise", "continued treatment", continuedTreatment);

scanScenarios = SimBiology.Scenarios("doseAmount", doseAmountValues);

combinedScenarios = add(doseScenarios, "cartesian", scanScenarios);

% Inspect scenarios:

generate(combinedScenarios)

% Create a simulation function for the model

simFun = createSimFunction(modelObj, combinedScenarios, "x", [], "AutoAccelerate", false);

% Simulate the model for every dosing scenario

simData = simFun(scenarios, 100);

% Plot the results

sbioplot(simData);

With the two repeat doses, you can also use the "Run Scan" program in the SimBiology Model Analyzer app to do the parameter scan over the dose amounts.

I hope this helps.

Best,

-Florian

[Zinnia Parra-Guillen]

Helps a lot! Thank you so much :)