Re: [SED-ML-discuss] Question about the sedml zip file

[Herbert S. <hs...@gm...>]

JDesigner currently supports it own annotation for storing multiple
data sets, has done for many years. I just thought there might be
something on the standards front  that I could use. I would have
thought however that SEDML would have been a convenient place to
reference parameter sets particularly for the use case I gave.
Simulation experiments need data so there has to be some link from
sedml to data sources, be in parameter sets or experimental data for
model fitting, or even statistical information on the the parameters
being used although parameter variability is now in SBML. I am sure
the sedml community has thought of this but I didn't find anything in
the draft to indicate this.

You could also include multiple parameter sets explicitly in Antimony.

Herbert

On Thu, Oct 6, 2011 at 4:12 PM, Lucian Smith <lp...@sp...> wrote:
> One of the goals of the distrib package is to allow you to store vectors
> that you choose from instead of single values.  But I *think* that the
> idea is to choose randomly from that vector, not to say 'use the first
> value in all vectors for this simulation, then use the second value in all
> vectors for the second simulation'.  Though I could be mistaken.
>
> If you want to wait for the 'arrays and sets' package, that might work.
> But it does suffer from the small drawback of not existing.
>
> I can imagine using comp for this, too (naturally).  In Antimony:
>
> model basemod(k1, k2)
>  S1 -> S2 + S3; k1*S1;
>  S2 -> S4;      k2*S2;
> end
>
> model set1()
>  basemod(k1, k2);
>  k1 = 3;
>  k2 = 10;
> end
>
> model set2()
>  basemod(k1, k2);
>  k1 = 10;
>  k2 = 3;
> end
>
> model set3()
>  basemod(k1, k2);
>  k1 = 7;
>  k2 = 7;
> end
>
> etc.
>
> I don't know if you can pick a particular model out of a file for
> simulation in SED-ML?  If so, that'd be all you need; if not, you'd need a
> file per set#() model.  (I wouldn't imagine it would be terribly difficult
> to extend SED-ML to do this, if it doesn't already.)
>
> -Lucian
>
> * Herbert Sauro <hs...@gm...> [2011-10-06 23:52] writes:
>> Nicolas, I looked up the SBML distrib package but unless I am mistaken
>> that seems to be related to specifying statistical data on parameters,
>> see
>>
>> http://sbml.org/Community/Wiki/SBML_Level_3_Proposals/Distributions_and_Ranges
>>
>> I want to be able to represent multiple parameter sets for a given
>> model, preferably named and with descriptions.
>>
>> How should I deal with this situation: Multiple parameter sets for a
>> given model where each parameter set needs a slightly different
>> simulation, eg different time end for a continuous simulation.
>>
>> Herbert
>>
>> >From 33K feet somewhere above continental USA.
>>
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> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
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