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Hello Nicolas,

As said before ... the multiple parameter sets annotation fulfills a need
right now ... in level 2 ... I'm perfectly aware of alternatives in Level 3.


As you know I'm especially interested in SED-ML. And this is in fact one
application for the multiple parameter set annotations. By simply marking
different parameter sets in applications like JDesigner (my library supports
these annotations and transforms them into the multiple parameter sets
annotation), or several other applications, these multiple parameter sets
will be transformed into SED-ML model and ChangedModel constructs, and
simplify the procedure of creating simulation experiments that showcase the
behavior of the model under the different sets.

Cheers
Frank

> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu [mailto:sbml-discuss-
> bounces@caltech.edu] On Behalf Of Nicolas Le novère
> Sent: Wednesday, February 24, 2010 1:56 PM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] Managing Multiple Parameter Sets in SBML
>
> Hi,
>
> I strongly believe that all initial conditions and parameter values will
> eventually have to be stripped of SBML. But that won't happen before
> Level4. Meanwhile, several mechanisms have been proposed so far. Lucian
> pointed out one possible way, i.e. the model composition package. Another
> one is the distributions and sets package. We will have to implement this
> package soon anyway, if we want to reach the drug discovery community
> (where the initial conditions are distributions). A third way is to use
SED-
> ML, i.e. to have a reference model, and to alter the values before running
> the simulation steps.
>
> Frank T. Bergmann wrote:
> > Dear SBML Community
> >
> > We often come across situations where it would be advantageous to have
> > more than one set of parameters included in a SBML model. This makes
> > it easy to store snapshots of parameter regimes in which a model shows
> different
> > behavior.
> >
> > In one of the SBML meetings in Tokyo we discussed this many years ago,
> > however there did not seem to be a consensus on how to store this sort
> > of information. What people ended up doing was to store the
> > information in proprietary annotations. As I was facing this problem
> > again recently, I ended up writing down the format of the annotation
> here:
> >
> > http://precedings.nature.com/documents/4233/version/1
> >
> > Perhaps, if there is enough interest we could think about building a
> > Level 3 package round it, or perhaps the groups package will be the
> > right place for this sort of information.
> >
> > The reason for me posting this information here, is of course that I'm
> > interested in seeing support for an annotation like this in other
> > software tools.
> >
> > Cheers
> > Frank
> >
> > ____________________________________________________________
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>
> --
> Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-
> Trust Genome Campus, Hinxton CB101SD UK, Mob:+447833147074,
> Tel:+441223494521
> Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nlenovere@hotmail.com(N
> OT email) http://www.ebi.ac.uk/~lenov/,
> http://www.ebi.ac.uk/compneur/, @lenovere
>
>
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>
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