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Robert Phair wrote:
> For Nicolas' particular cases:
>
> "More subtle:
>
> dx/dt = k * C * Y / (K + Y) where C = [calcium/calmodulin]/[total
> calmodulin]
>
> You would declare A as a modifier
>
> but
>
> dx/dt = k * P * Y / (K + Y) where P = pH
>
> You would not declare P as a modifier, but as a parameter
>
> Even if pH is in fact proportional to the concentration of H+"
>
> In the case of the reaction controlled by calcium:CaM, yes I would
> definitely expect calcium:CaM to be a species and to appear in the
> ListOfModifiers.

But the modifier is not calcium:CaM. It is the ratio between calcium:CaM
and total CaM. Therefore,
- either we define the ratio as a parameter and do not refer to it as a
modifier.
- or we declare both calcium:CaM AND total CaM as modifiers. Now, could-you
explain me how you draw a graph representing this situation?

> In the case of the pH-controlled reaction, if H+ is in the
> ListOfSpecies, but not in the lists of Reactants or Products for the
> reaction whose kinetic law you have written, then I WOULD declare H+ as
> a Modifier even if P were defined by
>
> P = -log[H+]

But modifiers are meant to correspond to the symbols in the kineticLaw. You
would end up with a modifier declaration pointing to H+ and a symbol in the
kineticLaw refering to P. 1) this is illegal SBML, 2) this is semantically
dodgy, 3) ... we go back to a situation where you have to analyse the
assignmentRule to fully understand the reaction! Which is precisely what
you criticised before.

> In the case of the assignment rule:
>
> "Consider the following assignmentRule:
>
> species A parameter X (not an entity pool) parameter Y
>
> if CONDITION 1 then Y = A else Y = X
>
> What is Y? "
>
> I don't think Y can be identified as a reactant, a product or a
> modifier.

Exactly. So if condition 1 is fulfiled, X represents a species, but you
would not declare it as a modifier.


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