Re: [SED-ML-discuss] Stochastic runs of CellML models?

[Chris J. M. <my...@ec...>]

One could use the BioCham approach to extract the reactions from the math like Mike does with the matlab to sbml converter.

Chris

Sent from my iPhone

> On Dec 20, 2015, at 2:29 PM, Lucian Smith <luc...@gm...> wrote:
> 
> That was actually going to be the next part of my question:  stochastic Reactions are a 'standard thing' in SBML, but I believe nobody ever tries to interpret the 'rate rules' in a stochastic manner.  If they did, that could presumably be applied to the CellML side of things.  Conversely, if CellML *did* have some sort of stochastic interpretation, the reverse could be true.
> 
> For now, it sounds like I should just not try to generate stochastic tests for CellML at all, and stick to reactions for SBML models.  Although if we want to explicitly claim that the SBML RateRule construct is 'immune' to stochastic simulations, I should include that, too.
> 
> -Lucian
> 
>> On Sun, Dec 20, 2015 at 12:09 PM, David Nickerson <dav...@gm...> wrote:
>> Hi Lucian,
>> 
>> Short answer - I'm not aware of any simulator that would know what to
>> do with a CellML model and a Monte Carlo simulation.
>> 
>> Long answer - something intelligent sounding about the math being
>> directly encoded in CellML vs the process description of SBML being
>> used to generate the math depending on your simulation algorithm (I
>> don't know if you can do a stochastic simulation of an SBML model that
>> only consists of math, no reactions?). Andrew Miller did have a
>> proposal for something along these lines with SED-ML, but requires
>> extra information provided for the CellML (or SBML) model
>> (distributions, ranges, etc.).
>> 
>> 
>> Cheers,
>> Andre.
>> 
>> 
>> On Sat, Dec 19, 2015 at 8:04 AM, Lucian Smith <luc...@gm...> wrote:
>> > So, SBML has a tradition of allowing the user to encode a single model, and
>> > allows you to simulate it deterministically or stochastically.  Does CellML
>> > have the same capability?  I'm obviously asking from the perspective of
>> > SED-ML--if the KiSAO terms for Monte Carlo simulation would mean anything to
>> > a CellML simulator.
>> >
>> > -Lucian
>> >
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>> 
>> 
>> --
>> 
>> 
>> David Nickerson
>> about.me/david.nickerson
>> 
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