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

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!

Answer 1

[Jeremy Huard]

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