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I feel that the community has a real need for multiple parameter set
now, I know because we have users that regularly use this facility. I
understand the hesitancy in this matter in order that the feature can be
resolved in the best way but I know that this will take a number of
years before it comes to fruition. In the mean time what do we do,
particularly with respect to Level 2 which is currently the dominant
level in use? Perhaps we can come to a bipartisan agreement, just like
they do in the US government, that is work towards a long term solution
that will be suitable for Level 3 but in the mean time recognize a
practical need for Level 2.

Herbert

Frank Bergmann wrote:
> 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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>> contact sbml-team@caltech.edu
>>
>
> ____________________________________________________________
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>
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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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