Re: Managing Multiple Parameter Sets in SBML
25 Feb '10 08:53
You are correct, the annotation does not address it. As far as the current
implementation is concerned with one click of a save button all parameters
of a model are stored as a new parameter set. This is mainly due to the
fact, that I would not like the user to have to choose which of his 300
favorite parameters he wants to consider to save.
As far as the implementation is concerned a parameter set could just as well
be a subset of parameters, or even just one parameter that could be applied
to the model. A parameter containing only of a subset of parameters is
considered equal to the set of all initial values defined for the model with
only the parameters in the subset being changed.
> -----Original Message-----
> From: firstname.lastname@example.org [mailto:sbml-discuss-
> email@example.com] On Behalf Of Dagmar Waltemath
> Sent: Thursday, February 25, 2010 12:14 AM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] Managing Multiple Parameter Sets in SBML
> Frank, I might have overread it in your proposal, but is your parameterSet
> complete set of all parameters?
> Or is the policy that a set can contain a subset of all model's
> only those are changed if the set is active?
> 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
> > 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
> > 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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