Re: Ancillary equations in SBML models
08 Aug '08 18:30
Sorry for rejoining the discussion so late.
raim> It would really help to clarify what the initial
raim> reasoning was to a) include listOfModifiers and b)
raim> to make it obligatory if a species appears in the
raim> kinetic law.
As I recall, the reason to require all species identifiers
appearing in a kinetic law to be listed in the list of
reactants/products/modifiers was simply the notion that this
would allow software tools to interpret the expressions
better. It's kind of the minimum sort of categorization
that can be done on species whose identifiers appear in an
(Aside, to reiterate what Nicolas already brought up: the
spec says the modifiers list should include all species
whose *identifiers* appear in the rate expression, not all
species that may affect the rate.)
raim> If the reason is to ensure that the chemistry is
raim> captured correctly, ie. that any species whose
raim> concentration modifies the rate should be in the
raim> list, then the rule should definitely be extended to
raim> species in rules. Although I agree that this can
raim> become complicated, when one rule refers to another
raim> rule etc.
I understand your point, and I think Pedro is arguing for
the same thing (if I understood Pedro's msg of August 6).
However, it's not immediately clear to me how you would do
it. Suppose a reaction R has a parameter A, whose value is
set by a rule A = f(B, C, ...) where B and C are species.
Should B and C be included in R's list of modifiers? If you
say yes, then where does this process stop? B and C, being
species, have their values determined by formulas which are
in effect rate rules, and *their* values may very well
depend on *other* species. It seems very possible that you
might end up with every species in the model listed as
modifiers of most reactions!
raim> Or does it have some practical reason, like
raim> generation of kinetic laws from SBO terms or
raim> something like that?
No, not that. SBO was invented after Level 2 Version 1 was
issued, where the list of modifiers was introduced.
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