[Miase-discuss] listOfModels query

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

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?
  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.
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.

  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??)
  // 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);

   // now use your model specific library to parse the altered model  
and run simulation.

  If we can clarify this I can put some examples into svn. I can send  
a class diagram if that would be more explanatory.

        Cheers
            Richard

-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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