Re: [Miase-discuss] listOfModels query

[Frank B. <fbergman@u.washington.edu>]

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