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David Nickerson wrote:
> Hi Andrew,
>
> This looks quite intriguing. As you mention later in this thread I
> currently take the approach of adding an extra real scalar term and
> exposing that as a way to hook future (in my case) currents into ion
> concentration rate equations. Such and approach works well when I only
> have three ion concentrations to deal with, but gets overwhelming when
> considering many different species, such as happens when adding
> metabolic processes to an electrophysiology model.
>
> Just to try and better understand your proposal by use of an example
> closer to my own work and perhaps to also check that this approach is
> not limited to metabolic models...
>
> Using this method, I would be able to say that each calcium membrane
> current is in the set of calcium fluxes and then formulate the time
> derivative of intracellular calcium concentration to be a sum over all
> fluxes in that set. Then as I extend the model I simply specify any new
> calcium currents as being in the set of calcium fluxes and the
> intracellular calcium concentration automatically has them included.
>
> Have I got that right?
>

That sounds right to me - metabolic modelling was indeed only a specific
example.

> Assuming I have understood this, how hard do you expect it to be to
> implement support for such set summation techniques in the current
> Auckland API implementation? I would guess this falls into the code
> generation services rather than the core API implementation?
>

I think that supporting CellML 1.2 will require additions to both the
core API implementation and the code generation services. Internally,
the code generation services don't have support for anything other than
scalars, and so adding in data types such as sets (and implementing
operators over them) will require some fairly significant internal
changes. However, there is no reason to believe that adding such support
is infeasible in the long term.

Best regards,
Andrew

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• [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Andrew Miller, 01/30/2008
  • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Michael Cooling, 01/31/2008
    • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Andrew Miller, 01/31/2008
      • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Michael Cooling, 01/31/2008
        • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Andrew Miller, 01/31/2008
          • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Michael Cooling, 01/31/2008
            • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Andrew Miller, 01/31/2008
            • [cellml-discussion] Using proposed CellML 1.2 features to create more re-usable metabolic models, Michael Cooling, 01/31/2008
  • [cellml-discussion] Using proposed CellML 1.2 features to createmore re-usable metabolic models, David Nickerson, 01/31/2008
    • [cellml-discussion] Using proposed CellML 1.2 features to createmore re-usable metabolic models, Andrew Miller, 01/31/2008

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