Combined Doses in Simfunction

Hi. I have the code below with two different target for dosing. I plan to use different values (input in the code for different doses) for thoses targets and use simFunction. How should I modify the code. Thanks

setup; %(I build the model here)
params ={'dose_amount','dose_amounta'};
Titles = {'plasma', 'lung','liver','kidney','muscle', 'skin','adipose','bone', 'brain','heart','spleen','pancreas','tumor'};
obs = {'V_tum'};
for i = 1:length(Titles)
    Title = Titles{i};
    entryAb =['CAb_' Title];
    entryADC =['CADC_' Title];
    entryPL =['CPL_' Title];
    entryPLun =['CPLun_' Title];
    obs = [obs;entryAb;entryADC;entryPL;entryPLun];
end
dis=linspace(5,70,numTumors);
for tumNum = 1:numTumors
    entryTVR ={sprintf('TVR_tum%d',tumNum)};
    entryAb ={sprintf('Ab_tum%d',tumNum)};
    entryADC ={sprintf('ADC_tum%d',tumNum)};
    entryPL ={sprintf('PL_tum%d',tumNum)};
    entryPLun ={sprintf('PLun_tum%d',tumNum)};
    obs = [obs;entryTVR; entryAb;entryADC;entryPL;entryPLun];
end
input = [0.5 0;0.5 0.5]*1E6*sbioselect(model, 'Name','BW').value/sbioselect(model, 'Name','MW_ADC').value;
sfxn  = createSimFunction(model, params, obs, {'plasma.ADC_plasma','plasma.Ab_plasma'},'UseParallel',true,'AutoAccelerate',false);
doseTable = getTable(d1);
doseTable1 = getTable(d2);
doseTables = [doseTable, doseTable1];
simData = sfxn(input,configsetObj.StopTime,doseTables);

%% Doses
d1 = sbiodose('d1', 'repeat');
d1.Amount = 'dose_amount';
d1.AmountUnits = 'nanomole';
d1.Interval = 'dose_interval';
d1.RepeatCount = 'dose_repeat';
d1.TargetName = 'plasma.ADC_plasma';
d1.StartTime = 0;
d1.TimeUnits=configsetObj.TimeUnits;
d2 = sbiodose('d2', 'repeat');
d2.Amount = 'dose_amounta';
d2.AmountUnits = 'nanomole';
d2.Interval = 'dose_intervala';
d2.RepeatCount = 'dose_repeata';
d2.TargetName = 'plasma.Ab_plasma';
d2.StartTime = 0;
d2.TimeUnits=configsetObj.TimeUnits;

Answer 1

[Jeremy Huard]

Hi @Mehdi,

If you want to use both doses for each simulation run, you will need a cell array of size 1xN, where N is the number of doses (here N=2).

You can refer to this doc page to learn about how to use SimFunction.

So, your code could look like this:

setup; %(I build the model here)
params ={'dose_amount','dose_amounta'};
Titles = {'plasma', 'lung','liver','kidney','muscle', 'skin','adipose','bone', 'brain','heart','spleen','pancreas','tumor'};

obs = "V_tum";
Titles = Titles(:); % make it column vector
obs_temp1 = ["CAb","CADC","CDL","CPLun"]; % keep it row vector
obs_temp1 = obs_temp1 + "_" + Titles;
obs_temp2 = ["TVR_tum";"Ab_tum";"ADC_tum";"PL_tum";"PLun_tum"]; % row vector
obs_temp2 = obs_temp2 + (1:numTumors);
obs = [obs; obs_temp1(:); obs_temp2(:)];

dis=linspace(5,70,numTumors);

%% Doses
d1 = sbiodose('d1', 'repeat');
d1.Amount = 'dose_amount';
d1.AmountUnits = 'nanomole';
d1.Interval = 'dose_interval';
d1.RepeatCount = 'dose_repeat';
d1.TargetName = 'plasma.ADC_plasma';
d1.StartTime = 0;
d1.TimeUnits=configsetObj.TimeUnits;

d2 = sbiodose('d2', 'repeat');
d2.Amount = 'dose_amounta';
d2.AmountUnits = 'nanomole';
d2.Interval = 'dose_intervala';
d2.RepeatCount = 'dose_repeata';
d2.TargetName = 'plasma.Ab_plasma';
d2.StartTime = 0;
d2.TimeUnits=configsetObj.TimeUnits;

doses = [d1,d2];

%%
input = [0.5 0;0.5 0.5]*1E6*sbioselect(model, 'Name','BW').value/sbioselect(model, 'Name','MW_ADC').value;
sfxn  = createSimFunction(model, params, obs, doses,'UseParallel',true,'AutoAccelerate',false);
doseTables = getTable(doses); 
simData = sfxn(input,configsetObj.StopTime,doseTables);

Note that I use strings to build the observable names.

EDIT: changed code to use the doses array.

[Mehdi]

Hi,

Thanks for your reply. When I apply both does as you suggested I see the error below:

code:

sfxn  = createSimFunction(model, params, obs,{'plasma.ADC_plasma','plasma.Ab_plasma'},'UseParallel',true,'AutoAccelerate',false);
doseTable = getTable(d1);
doseTable1 = getTable(d2);
doseTables = {doseTable, doseTable1};
simData = sfxn(input,configsetObj.StopTime,doseTables);

error:

Error using SimBiology.function.SimFunction/verifyU
Each column of the dosing information table must be a numeric vector.

Error in SimBiology.function.SimFunction/validateAndStandardizeFevalInputArguments (line 550)
                    verifyU(obj, scenarioDoseTables, u);

[Jeremy Huard]

I had not seen that your doses are parameterized doses, namely their amounts is defined with a parameter.

For SimBiology to know that the dose are parameterized, you will need to pass the dose objects to createSimFunction and not the dose targets:

sfxn  = createSimFunction(model, params, obs,[d1,d2],'UseParallel',true,'AutoAccelerate',false);

[Jeremy Huard]

Btw, you can make the code more compact with the following:

doses = [d1,d2];
sfxn  = createSimFunction(model, params, obs, doses,'UseParallel',true,'AutoAccelerate',false);
doseTables = getTable(doses); 

Answer 2

[Mehdi]

Can anybody help?