Re: [Miase-discuss] sed-ml library?

[Nicolas Le N. <le...@eb...>]

Frank Bergmann wrote:

>>         3) Could a model file be optionally  embedded in a sedml file?
>>   This gets round the need to keep sedml independent of sbml, also a
>> single file gets round the file coordination issue,  but it raises new
>> problems of keeping in synch possibly multiple copies of a model. But
>> for non-curated models that must be an issue anyway?
>>
> 
> personally I don't like this option too much. If an embedding solution 
> is wanted, I prefer it to work the other way around, have MIASE embedded 
> in i.e. SBML. That is the solution  that was favored by some people in 
> the discussions as well. 

Yes, but that would preclude the use of SED-ML for using two different external models. At the moment, we only use two models for comparing them. But nothing precludes the post-processing of the simulation results of one model using variables coming for another model. Same thing for the changeMath definition. We will be able to modify a model prior to a task by using values coming from another model.  

But more importantly, with SED-ML one can define a simulation experiment using both SBML and CellML models (or VCML etc.) Several groups are working on integrating different formalisms. The approach is generally to import the different model to have an internal integrated view. SED-ML would offer an alternative in some case, where the integration could be done at run-time. We have actually a real-case in the group (although not using CellML and SBML). On PhD here is running hybrid simulations of neurons, with electrical and biochemical representations. The models are defined separately, because using completely different formalisms. The integration is done at run-time, with some variables of a simulation affected by the variables of the other one.

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust 
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