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Tom Morse wrote:
> Dear CellML'ers,
>
> I wanted to solicit your feedback on an invited article I wrote for
> Scholarpedia late last week on model sharing in computational neuroscience:
>
> http://www.scholarpedia.org/article/Model_Sharing_in_Computational_Neuroscience
>
The page you linked says the CellML stands for "Cell Markup Language". I
note that some other external papers and websites have used this
expansion. However, this is not very accurate, because CellML doesn't
really 'mark up' cells, it only describes the mathematics.

You also say, below a list including CellML: "Each of the above sites
started out with a particular domain of interest, for example ModelDB
(Olfaction) and Visiome (Vision
<http://www.scholarpedia.org/article/Vision>), and Biomodels and DOQCS
(Cell Signaling Pathways), and have subsequently expanded to broader
categories of neuroscience and biological mathematical models."

However, CellML didn't really start out modelling a particular domain.
CellML has always been intended as a generic way to represent
mathematical models (although, as the name implies, it was initially
developed by groups with an interest in representing biological models,
and its use in practice has been for biological mathematical models).

I would also suggest that you mention metadata specifications (in terms
of annotating parts of the model, linking them to other databases, and
other machine-readable data describing how a model relates to reality).

The need for sharing information needed to create and validate models is
also a major area. In particular, it would be worth mentioning the
information in box 3 in:/ "Nature Biotechnology/ *23*, 1509 - 1515
(2005) Minimum information requested in the annotation of biochemical
models (MIRIAM); Le Novere et. al.", as many existing models would
become more sharable were all the criteria met.

Best regards,
Andrew

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• [cellml-discussion] new scholarpedia article on model sharing in computational neuroscience, Tom Morse, 04/03/2007
  • [cellml-discussion] new scholarpedia article on model sharing in computational neuroscience, Andrew Miller, 04/03/2007
  • [cellml-discussion] new scholarpedia article on model sharing in computational neuroscience, Tommy Yu, 04/03/2007

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