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[cellml-discussion] [Tracker Item 42] New: CellML1.1.1specification


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  • From: ak.miller at auckland.ac.nz (Andrew Miller)
  • Subject: [cellml-discussion] [Tracker Item 42] New: CellML1.1.1specification
  • Date: Wed, 18 Jul 2007 17:27:09 +1200
David Nickerson wrote:
> Hi Matt,
>
>
>> I think there does need to be some description of what the parts of a
>> cellml specification version number is and how it relates to the
>> cellml namespace(s).
>>
>> My understanding is that the 1.1.1 was chosen so that this did
>> represent a minor step in thinking for CellML 1.1, but that the model
>> remains valid as a 1.1 model. i.e. A CellML 1.1 model is not
>> necessarily a valid 1.1.1 model and a migration step would be needed
>> to make it so. The namespace of a 1.1.1 model would still be
>> http://www.cellml.org/cellml/1.1#
>>
>> I also think that this minor version should be marked in glaring red
>> that it is precisely a depreciation of reactions step and provide
>> reasons why and the tools to help people transform any models they
>> have with reactions into ones that don't. I think there will be some
>> debate around that - especially pointing to lossless transforms
>> between SBML and CellML and back again with existing transforms
>> available out there.
>>
>> My assumption would be that CellML 1.2 or 2.0 namespace would be the
>> one where reaction elements become invalid if indeed 1.1.1 was
>> successful.
>>
>
> you seem to be saying that version 1.1.1 is marking the reaction element
> for deprecation but that the reaction element itself won't become
> invalid until a 1.2 or 2.0 version is released? This doesn't seem to
> match with completely removing all reference of and to reaction elements
> in the 1.1.1 specification...maybe I'm missing something?
>
1.1.1 doesn't describe the reaction element, but 1.1 does, and 1.1.1 and
1.1 are in the same namespace. If software which has supported reactions
per the CellML 1.1 specification sees the reaction element, it will
follow the 1.1 specification (indeed, we probably would benefit from an
implementation guide which encourages tool developers to support more
than one version of CellML if possible. How many versions back they want
to support is up to them).

Model authors on the other hand will be strongly encouraged to use
CellML 1.1.1.

Best regards,
Andrew



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