Re: stoichiometries of modifiers - is SBML too "narrow"?
26 Apr '05 14:12
Pedro Mendes wrote:
> On Monday 25 April 2005 10:14 pm, Howard Salis wrote:
>>I think the idea of 'modifiers' is too vague to be useful.
> I think the discussions in this list are starting to convince me that anyone
> who wants to be doing any modeling of biochemical systems should first have
> to pass an "Enzyme Kinetics" course. The concept of modifier is not vague
> at all, it is quite well defined.
I personally think that people doing biochemical network modelling
should be able to explain why classical continuous deterministic enzyme
kinetics is both irrelevent and wrong! ;-)
Seriously though, I think that this thread illustrates a genuine problem
within the "SBML community" which needs to be addressed in order to
avoid a split. The fact is that most of the people involved in the
development of SBML, and most of the people responsible for the
continuing development of SBML, are people with backgrounds in
continuous deterministic modelling, and the SBML specification obviously
reflects that. On the other hand, much of the most interesting and
innovative work being carried out in the biochemical network modelling
field at the moment does not fit into that framework. If the guardians
of SBML are not prepared to consider how the format can develop in a way
that is inclusive of other modelling paradigms and kinetic theories, I
am not optimistic that SBML can continue to dominate as a framework for
representation of biochemical network models.