Re: Ancillary equations in SBML models
05 Aug '08 08:51
Robert Phair wrote:
> The L2v3r2 specification (p. 66) says:
> "4.13.2 The SimpleSpeciesReference abstract type
> As mentioned above, every species that enters into a given reaction must appear in that reactionâ��s lists of reactants, products and/or modifiers."
I agree that modifier definition is hanging loose a bit within the SBML
framework. But i might also not think across the whole range of purposes
of SBML. Please correct me here, I am not so familiar with other then
SBML describes the chemical reaction network, for the main purpose (?)
to reproduce the construction of mathematical models from such networks.
Most SBML specifications and obligatory rules ensure that this
conversion is always possible without loss.
However, the modifiers are not required for e.g. conversion to
differential equation systems.
Are they required e.g. for other mathematical derivates of the SBML
reaction network, e.g. for constructing stochastic or mass-action models
from enzyme models? Otherwise, the obligatory list of modifiers exists
not for the construction of the math, but for construction of the graph
- would that be correct?
And in that it seems to be unique among SBML specifications.
In any case, the current obligatory listing of modifiers of a reaction
can always be easily circumvented by using - e.g. simple assignment
rules (M_rule = M) - a fact that somehow undermines the obligatory list
of modifiers. In principle, I would support to extend the obligation to
list modifiers to species in rules and function definitions used in the
But maybe, it should first be clarified for what purpose the modifiers
are obligatory in the first place: math/kinetics, graph/structure or for
Maybe it is worthwhile to distinguish these two requirements for an SBML
model: a) allow correct and easy conversion to math, but b) ALSO
represent the chemical reaction network in the best possible detail
(independent of both the graphical extension and the requirements for
unique math conversion).
The latter point is certainly a bit fluffier and highly dependend on the
scale and context of the model, considering e.g. biochemists urging for
inclusion of protons.
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