Combined Doses in Simfunction
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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;
采纳的回答
Jeremy Huard
2024-5-6
编辑：Jeremy Huard
2024-5-6
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).
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.
3 个评论
Mehdi
2024-5-6
Jeremy Huard
2024-5-6
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
2024-5-6
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);
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