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I think in the current repository framework, variants are probably the
way to go if you really want to have all the different cell types
represented. However, if the only differences are parameter value
changes then I'd be tempted to simply describe those changes in the
model annotation/documentation and have just the one model in the
repository to avoid cluttering the repository any more than necessary.

As Matt mentioned, the obvious solution is to use CellML 1.1 and import
the base mathematical model into the different parameterisation models.


Andre.

James Lawson wrote:
> Addendum:
>
> The model in the repository describes the apex cells only.
>
> James Lawson wrote:
>> Hi folks,
>>
>> I'm just fishing for some comments on how to handle cases where there
>> are models which describe, for example, the properties of multiple cell
>> types. Bondarenko et al. 2004 is a good example of this:
>>
>> "In the Bondarenko et al. 2004 publication described here, the authors
>> develop a computer model of the mouse ventricular action potential (see
>> below). The model includes parameters for both the apex and the septum
>> regions of the heart (the apex parameters have been substituted into the
>> CellML version of the model described in ), and this helps to illustrate
>> how there are regional differences in myocyte repolarisation in the
>> mouse heart."
>>
>> Penny Noble has just sent me a zip file containing the latest versions
>> of all the models she has curated for COR. I'm currently in the process
>> of comparing these versions to the latest versions we have on the
>> repository. In some cases, she has provided several variants of the same
>> model which describe different cell types, as above.
>>
>> Firstly, are these true 'variants'? If so, then the matter is relatively
>> simple. Unfortunately, if one goes through the repository list, variants
>> simply come up as a duplication of the model listing, with no
>> information concerning what the variant represents. This is something I
>> imagine will be fixed in time, but is presently rather frustrating
>> considering the issue at hand.
>>
>> Does anyone have any comments on this? Should I simply put the files up
>> as different variants, with a note in the documentation?
>>
>> Thanks,
>> James Lawson
>> _______________________________________________
>> cellml-discussion mailing list
>> cellml-discussion at cellml.org
>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion

--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg

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• [cellml-discussion] model variants(?): e.g. where multiplecelltypes are described by the same model in different files, (continued)
  • [cellml-discussion] model variants(?): e.g. where multiplecelltypes are described by the same model in different files, David Nickerson, 04/12/2007
  • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, James Lawson, 04/12/2007
    • [cellml-discussion] model variants(?): e.g. where multiple celltypes are described by the same model in different files, David Nickerson, 04/12/2007
      • [cellml-discussion] curation annotation framework, James Lawson, 04/12/2007
        • [cellml-discussion] curation annotation framework, David Nickerson, 04/12/2007
        • [cellml-discussion] curation annotation framework, James Lawson, 04/12/2007
        • [cellml-discussion] curation annotation framework, Matt , 04/12/2007
        • [cellml-discussion] curation annotation framework, David Nickerson, 04/12/2007
        • [cellml-discussion] curation annotation framework, David Nickerson, 04/12/2007
    • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, Matt , 04/12/2007
  • [cellml-discussion] model variants(?): e.g. where multiple celltypes are described by the same model in different files, David Nickerson, 04/12/2007

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