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Hello Pedro,

I agree with you on all your points as I have with Bob :)

However I can not see a way that SBML and its supporting tools can
enforce that all MODIFIERS are listed. This is obvious for SBML models
which do not have any kinetic information. In such a model the
requirement is unenforceable and it is up to the modeller to provide a
complete list.

Even in the presence of kinetic information the examples in this thread
indicate that the meaning of the word modifier is not properly defined
and thus analysing the dependencies (including all indirect) of the
kinetic law will not suffice.

If we want to enforce a complete list of MODIFIERS for SBML models
where this is applicable (models with complete kinetic information) we
have some work to:

1) Define what is a MODIFIER in SBML terms.
2) Implement checks in tools which verify the completeness of the
MODIFIERS for applicable models.

Assuming we succeed in defining a MODIFIER in SBML e.g. based in the
definition in SBO:
Substance that changes the velocity of a chemical reaction without
itself being consumed or transformed by the reaction.

we will still be faced with ambiguous situations as in Nicolas' example:

Y -> X;
K is specified as modifier;
k is constant
v = k * C * Y / (K + Y)
C = [calcium/calmodulin]/[total calmodulin]

Under the assumption that we mapped substance in SBO to a species in
SBML, we have dependent on the choice of the modeler for the entities
calcium, calmodulin, and "total calmodulin" different list of
modifiers. This means we need to define rules which specify whether an
entity is a species or a parameter. Even if we succeed in defining
those I see no way to enforce them without further semantic information
(e.g. SBOterm) in SBML, which again is up to the modeller to provide.

If we remove all these ambiguities 2) becomes a trivial task and most
simulators must have already implemented them in some way to correctly
calculate the kinetic law.

We need to decide whether it is helpful to have rules which can not be
enforced. In my opinion a rule which can not be enforced is
meaningless since we can not rely on it. Thus the only way out is the
agreed upon best practise document.

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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