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Nicolas Le novère wrote:
>>
>> | dx/dt = k * C * Y / (K + Y) | where C = [calcium/calmodulin]/[total
>> calmodulin]
>>
.....
>
> If C was in the listOfSpecies, since it is in the kineticLaw, it would be
> in the listOfModifiers.
>

It might be better to move the currently existing modeler's or
software's choice of what is a modifier and what not, to exactly this
point:
define it as a parameter or a species. If defined as species, then it
should be in the modifier list, even if it just appears in a rule and
not explicitly in the kinetic law.

So for above example, one could choose both calcium and calmodulin as
species (and thus modifiers), while C and "total calmodulin" are derived
parameters.
They are all in concentration units though, and the derived entities
could as well be defined as "species" in another model's context: this
should be the modeler's choice.

I think this could be less ambiguous then the current state, where the
modeler might not even have control on whether a species will appear
explicitly in the kinetic law or not, depending on the software
generating the math (ok, then it's a software problem again ;).


> Sorry, but if there are no kineticLaw, the concept of modifier is moot.
> Even if the modifier was listed, the reaction would be "incompletely
> specified".
>
> Reactant A
> Product B
> Modifier C and D
>
> What does that mean? What is the effect of C and B? Are they stimulators?
> Inhibitors? Neutral? Have opposite effect?

Actually that could be quite common: the exact kinetics are not known
yet, but the modifiers are (is it competitive or non-competitive
inhibition e.g.). And thus the modeler leaves kinetic law empty, e.g.
for other software to infer the exact form of the kinetic law from
measurements.

Rainer
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