Re: [sbml-comp] [libsbml-development] Comp package: Have a species in one submodel replace a species in another submodel?

[Lucian S. <luc...@gm...>]

You are exactly correct:  you need to provide local copies of things that
can then replace or be replaced by elements in the submodels.  To recreate
your situation in Antimony:

model model1()
  species A in comp1, B in comp2
  A -> B;
end

model model2()
  species C in comp3, D in comp3
  C -> D;
end

model combined()
  //Declare the local species and compartment:
  species C2 in cMain

  //Import the other models as submodels:
  M1: model1()
  M2: model2()

  //Connect the compartments and species
  M1.comp2 is cMain
  M2.comp3 is cMain
  M1.B is C2
  M2.C is C2
end

Which in SBML would be the attached model (though presumably with external
model definitions instead of local ones).

This version used the 'replacedElement' constructs, but you could also pick
one of them and used the 'replacedBy' construct.  In that case, any
initialConcentration or other attribute value would be taken from the
submodel target of that replacedBy, instead of by the parent model.

-Lucian

On Tue, Jan 20, 2015 at 4:25 AM, Daniel Palm <pa...@gm...> wrote:

> Dear all
>
> Suppose I have two external models that I cannot change (well, I can, but
> it's undesirable for a number of reasons):
>
> model1:
>
> A -> B
>
> model 2:
>
> C -> D
>
> I want to combine these, but B and C are actually the same species and in
> the same compartments. The final model should look like this
>
> model_combined:
>
> A -> C
> C -> D
>
> with A in compartment 1 and C and D in compartment 2.
>
> Am I right that the only way would be to have model1 and model2 as
> submodels of another model. And make a new compartment that replaces that
> of B, C, and D, and make a new species C that replaces B and the old C?
>
> It would be nice if I could simply say somehow that C (model2) replaces B
> (model1) and that the compartment of C replaces the compartment of B. Is
> this possible?
>
> I would be grateful for any help.
>
> Best regards
> Daniel
>
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