Export initial conditions of parameters​/compartme​nts/specie​s into workspace

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Justine
Justine 2024-1-4
编辑： Jeremy Huard 2024-1-10
Hello,
I have built a PBPK on Simbiology (2023b), with numerous parameters and compartments whose values are mostly defined by initial assignements. I nicely see the initial conditions in the model builder app after activating the initial conditions button in the toolbox. I usually have 1 by default in the value column and my calculated value based on the initial assignements in the initial conditions column.
However, when exporting the model to MATLAB Workspace (via Model tab > Export > Export Model to MATLAB Workspace), I cannot retrieve the initial values, but only the default 1 values appear.
Is there a way to access the initial values in the MATLAB workspace to do some calculations? (both for parameters and compartments)
Or, maybe even better, is there a way to transfer the initial conditions to values, as they remain constant ?
Thank you very much in advance!

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Jeremy Huard
Jeremy Huard 2024-1-4
编辑：Jeremy Huard 2024-1-10
Ran in:
Dear @Justine,
there is currently no built-in command line interface to get the initial conditions.
However, you could simulate the model with StopTime=0 to get these values.
I have attached an implementation of this approach (sbiogetInitialValues.m) that returns both a table and a variant with the computed initial values.
Here is an example:
s = sbioloadproject('lotka.sbproj');
modelObj = s.m1;
modelObj.Species
ans =
SimBiology Species Array Index: Compartment: Name: Value: Units: 1 unnamed x 1 2 unnamed y1 900 3 unnamed y2 900 4 unnamed z 0
% let's now add initial assignments and check the initial values
addrule(modelObj,'x = z','initialAssignment');
addrule(modelObj,'z = 100','initialAssignment');
[tableOut, variantOut] = sbiogetInitialValues(modelObj)
tableOut = 8×4 table
Type Name Property Value _______________ ________________ _________ _____ {'compartment'} {'unnamed' } {'Value'} 1 {'species' } {'x' } {'Value'} 100 {'species' } {'y1' } {'Value'} 900 {'species' } {'y2' } {'Value'} 900 {'species' } {'z' } {'Value'} 100 {'parameter' } {'Reaction1.c1'} {'Value'} 10 {'parameter' } {'Reaction2.c2'} {'Value'} 0.01 {'parameter' } {'Reaction3.c3'} {'Value'} 10
variantOut =
SimBiology Variant - Initial values (inactive) ContentIndex: Type: Name: Property: Value: 1 compartment unnamed Value 1.0 2 species x Value 100.0 3 species y1 Value 900.0 4 species y2 Value 900.0 5 species z Value 100.0 6 parameter Reaction1.c1 Value 10.0 7 parameter Reaction2.c2 Value .01 8 parameter Reaction3.c3 Value 10.0
I hope this helps.
Best regards,
Jérémy

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