Re: [Miase-discuss] listOfModels query

[Richard A. <ra...@st...>]

Oh great,
  That all sounds fine then.
  I'll try to look at your example next week Dagmar.

  Frank, so you mean something like:

   String   sedMLDoc.getModel(String modelId);

    which would hide all the need for getting XPath terms, and return  
a String of the model? That would be more direct, for sure.

  Richard

> Just to say that I agree with everything Frank wrote (hopefully I
> understood right what he meant ;-)).
>
> Dagmar
>
>
>
> Frank Bergmann wrote:
>> Hello ...
>>
>>
>>> Hi,
>>>   Just a query about the listOfModels element - is it assumed to be
>>> the case that, for a given sedml document, it will describe a single
>>> 'reference' model version, which will be the first model in the list,
>>> and subsequent entries in the list will refer to that base model,
>>> applying changes (as is the case with the example 'oscillation to
>>> chaos' model)? Or, is it possible that a given sedml document could
>>> refer to >1 reference model?
>>>
>>
>> Definitely ... you can (and should be able to) refer to more than one model.
>>
>>
>>
>>>   I'm asking from the point of view of how a self-contained .miase
>>> archive file might look. (By self contained, I mean that the
>>> application using it will be able to access all the information needed
>>> to run a simulation without having to query repositories -  with the
>>> help of a supporting library. ) In the first case above,  it would
>>> only ever contain a single model file, in the second case, it could
>>> contain multiple models.
>>>
>>
>> In my implementation, the self-contained .miase file, still has the option
>> of referring to external sources. Thus There could be 0 or more models
>> contained in the archive.
>>
>>
>>> Also, do we want to allow archives which contain all model variants as
>>> complete models, or are we going to stick with a 'reference' version
>>> of the model, and generate new, altered versions of the model by
>>> applying Xpath changes on the fly at runtime? I assume the latter, but
>>> I can't find anything in the current examples, or in the CMSB2008.pdf
>>> to distinguish between these possibilities.
>>>
>>>
>>
>> I hoped to keep the .miase file as simple as possible. It really just
>> provides the option of storing (locally) referenced files conveniently.
>> Apart from that there should not be more logic needed to interpret a .miase
>> file, as compared to the original experiment description. For that reason
>> I'd opt of making the changes on the fly, they won't be expensive to do.
>> While writing out you can opt to refer to the altered models if you so
>> desire, however with that you loose the information, that the second model
>> is actually the first model with a handful of changes ...
>>
>>
>>>   From the point of view of supporting library methods, I was thinking
>>> something along the lines of:
>>>
>>>   MiaseArchive archive = libSedml.readArchive(String
>>> filepathToMiaseArchive);
>>>
>>>   // A MiaseArchive enables access to a sedml document, and model
>>> file(s?)
>>>   SedmlDocument document = archive.getSedMlDocument();
>>>   // access Sedml DOM via
>>>   document.getSedMlModel();
>>>
>>>   //access model file ( or is it possible to have > 1 model file
>>> here??)
>>>
>>
>> YES it is ... :) ...
>>
>>
>>>   // if the latter, need method to iterate over multiple model files.
>>>    String referenceModelContents = archive.getModelAsString();
>>>
>>>    //now, get XPath change from SedML model and apply it
>>>    ListOfChanges changes =
>>> sedMl.getListOfModels.getModelById(modelID).getListOfChanges();
>>>    String alteredModelContents =
>>> document.applyChanges(referenceModelContents,changes);
>>>
>>>
>>
>> Instead of
>>
>> 	document.applyChanges(referenceModelContents,changes);
>>
>> I'd prefer to just grab the changed model. That's what I did in my
>> implementation, for a user there is hardly a difference on the two model
>> types. Thy have the option of getting the model source from both, and in
>> that case the changed model, applies the changes automatically.
>>
>> Best
>> Frank
>>
>>
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-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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