Forums

* shoops <shoops@vbi.vt.edu> [2010-02-24 22:05] writes:
> Hello Lucian,
>
> On Wed, 24 Feb 2010 21:41:05 +0000
> Lucian Smith <lpsmith@spod-central.org> wrote:
>
> > The obvious candidate to store this information for me is the
> > Hierarchical Modeling package. It won't store everything in one
> > file, but it would make it possible to store a series of 'wrapped'
> > models, each with a different parameter set, but based on the same
> > underlying model.
> >
>
> This is not true. In the hierarchical modeling package the model can be
> internal or external. Thus everything in a single file is possible.

We're starting to drift off-topic from Frank's original question, but what
I meant was that since the Hierarchical Modeling package for L3 is meant
to be 'flattenable' to a single L2/L3 model, you could not encode multiple
initial parameter values in a single SBML file. (At least, as I
understand it?) One might implement it as:

File 1:
The full model, with the first set of initial conditions.
File 2:
A reference to File 1.
Replacements for any element you wanted new initial conditions for
File 3:
A reference to File 1.
Replacements for any element you wanted new initial conditions for

Etc. Each file apart from the first would be pretty small, but you'd
still need multiple files.

I think if you wanted multiple models in a single file (and wanted to use
HM to do it), you'd have to hack the system--perhaps a base-level model,
a model above that that replaced some bits, a model above *that* that
replaced the same bits, etc. If you flattened it, you'd only get the
'top-level' model, but you could abuse the system by pulling out the inner
ones for this purpose. I think that's probably the wrong thing to do, but
would be willing to be convinced otherwise.

-Lucian
____________________________________________________________
To manage your sbml-discuss list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the sbml-discuss list,
contact sbml-team@caltech.edu