RE: thoughts on models and and model parameters
09 Dec '02 02:24
on Pedros comments:
I agree that:
>parameter sets only
>exist in the context of a model.
however this doesn't mean that more than one set of
parameters is meaningful for the same model. In fact
this becomes a very meaningful way to represent mutants.
An additional application (which might be close to Pedro's heart)
is using parameter sets to store the results of different
parameter optimisation/fitting runs on the same model.
[Whilst I can see that a modeller can use a database of
experimental results directly (across several models) my
impression is that
a significant part of the modeling community is not doing
this i.e. there is a significant amount of massaging,
optimisation and guessing going on that seperates
the raw experimental results from the parameters
used in models. However I don't know this from
direct experience. I'm interested in knowing more about
other peoples experiences.]
I think we can make parameter sets a seperate standard
that references sbml models. At worst parameter sets
would be in a rdf element(?) in a seperate XML namespace
in the same stream/file as the model. At best the
parameter set would be in a seperate file.
I think we should not encourage the use of parameter sets
in publishing contexts at least until the dust settles on this
issue with wide adoption in software.
I guess that all we need in SBML L2 is parameter value
and species initialAmount to be optional.
It is clear that different tools are going to have to
do there own validation of some aspects of SBML.
eg presence of parameter values.
However I would hope that parser libraries could
have a function like checkHasValues which raises
errors if parameter values and species initialAmounts are left out.
Later paraser libraries could do parameter value resolution from
a 'stack' of parameter sets that are applied to a given model.
> -----Original Message-----
> From: firstname.lastname@example.org
> [mailto:email@example.com] On Behalf Of Pedro Mendes
> Sent: 07 December 2002 22:43
> To: firstname.lastname@example.org
> Subject: Re: [sbml-discuss] thoughts on models and and model
> > So, for me at least, I don't see the model and its
> parameter values as
> > being separable at all. It may be a long term issue though (i.e.,
> > return to in 2010) and something that will be more relevant
> to protein
> > interaction-based networks versus metabolic networks et cetera.
> Actually I also agree that parameters and models are not
> independent. This is as true in metabolic networks as it is
> in protein binding networks. It turns out that enzymatic
> activity depends upon substrate binding to enzymes and this
> is also a spectrum of values (i.e. most dehydrogenases can
> use NADPH and NADH with different affinities, though some are
> small enough that we donīt usually consider the alternate
> substrate, but even this may be relevant at times)
> Although models may be incomplete as some parameter values
> are not known (or uncertain), isolated parameter sets are
> completely meaningless. This is because parameter sets only
> exist in the context of a model. So even if one could have
> models with several parameter sets, there will never be a
> parameter set that applies to two models. This means, from a
> computational point of view, that making parameter sets
> independent from models is not useful. So, we have arguments
> from both the biochemical and computational sides to refuse
> this idea of separating parameter values from models.
> looking forward to a lively workshop!
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