Forums

JDesigner stores multiple parameter sets relative to a single model (all
in one file). SBML files are verbose as it is so I didn't want to
repeatedly store the same model multiple times. I know there are users
who use multiple parameter sets in JDesigner quite extensively. Each set
has an Id, the parameters (including initial conditions) with values and
a notes section. Parameter sets can be restored or saved as need be.

Herbert

Lucian Smith wrote:
> * Frank Bergmann <fbergman@u.washington.edu> [2010-02-24 21:16] writes:
>
>> 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 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.
>
> Would that be sufficient for your envisioned use cases, or is there a
> distinct advantage to putting multiple versions of a model in a single
> file?
>
> -Lucian
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--
---
Herbert M. Sauro, PhD
Associate Professor
Department of Bioengineering

University of Washington
William H. Foege Building
Box 355061
Seattle, WA 98195-5061
206.685.2119 (tel)
206.685.3300 (shared fax)
http://www.sys-bio.org

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