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> If two models contradict each other (such as by each stating a
> initial value for concentrations of the same species, or a different
> mechanism for the exact same reaction), then this contradiction has
> to be fixed before the models can be composed.

It's not just about composition - during model simulation work often
initial conditions are altered before running. If we had two (or more)
'substances' that actually relate to the same substance, it would be
easy to make a contradiction after the model has been composed just by
altering one of those initial conditions.

> I am therefore focusing on clean ways to compose non-contradictory
> models which involve some overlap of chemical species (and so the
> assumption is that the initial values are the same).

I wonder if in general allowing duplications is not the best we could
do. Especially if we hope to build larger models from smaller ones
with the least cellml code editing (including resetting initial
conditions).

I think as well the good work you have done here it would be valuable
to explore as an extension ways of resolving such conflicts possibly
with cellml language elements, or at least not advocating the creation
of higher level structures which could easily leads to such conflict
(not that we can prevent people building them if they try hard enough
:) ).

Metadata and tools contribution to the model composition process
notwithstanding.


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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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