More generally I think this issue is tapping on the bigger issue of a
core modelling language and specification, and then special use cases,
of which biological modelling would be a particular case of.
Without reactions, we pretty much have that core language.
My inclination is that biological mo
David Nickerson wrote:
> Matt wrote:
>>> It seems there is some misunderstanding as to whether we are discussing
>>> a proposal to remove the reaction element from CellML or a proposed new
>>> specification. I thought it was the latter but you seem to be talking
>>> about the former...
>>
>> Both.
> > If we had our specification in a version control system and tagged
> out
> > releases and release candidates etc, and if we followed a protocol of
> > releasing at least one stable minor release that marks depreciation
> > only, then the following would be the result (in my mind)
> >
> > - The
Matt wrote:
>> It seems there is some misunderstanding as to whether we are discussing
>> a proposal to remove the reaction element from CellML or a proposed new
>> specification. I thought it was the latter but you seem to be talking
>> about the former...
>
>
> Both. I think.
>
> So I will try
>
> It seems there is some misunderstanding as to whether we are discussing
> a proposal to remove the reaction element from CellML or a proposed new
> specification. I thought it was the latter but you seem to be talking
> about the former...
Both. I think.
So I will try another explanation.
I
> I'm not pretending to understand the CellML version numbering system,
> but to serve as an example, would you be suggesting that changes such
> as removing a reaction element are a proposal for a future say 1.2
> versions where the namespace is changed?
yes. assuming there is a 1.1.1 (or 1.1a) s
Hi Poul,
That makes sense to me - although I would call it 1.1.1 rather than 1.1a
which to me implies an alpha pre-release of 1.1.
Andre.
Poul Nielsen wrote:
> Dear all
>
> I think that we are in agreement about the need to signal to the
> CellML community that the reaction element is depre
Dear all
I think that we are in agreement about the need to signal to the
CellML community that the reaction element is deprecated. As I
mentioned at the CellML meeting, I favour doing this by formally
indicating so in the specification. I appreciate that some would like
to move quickly on
Hi Andre,
I'm not pretending to understand the CellML version numbering system,
but to serve as an example, would you be suggesting that changes such
as removing a reaction element are a proposal for a future say 1.2
versions where the namespace is changed?
Also, if there is something we call the
> I think that we disagree about how the specification process should work
> and what it aims to address. I see a given version of a CellML
> specification as being a 'protocol' which both tools and model authors
> speak, therefore allowing them to interwork.
All I'm trying to point out is that
David Nickerson wrote:
>> Correct me if I am wrong, but I believe that nothing in the text of the
>> CellML 1.1 specification says that reactions will or will not be
>> deprecated in any future version of CellML, and therefore there is no
>> need for an erratum to CellML 1.1 (and indeed, such an
> Correct me if I am wrong, but I believe that nothing in the text of the
> CellML 1.1 specification says that reactions will or will not be
> deprecated in any future version of CellML, and therefore there is no
> need for an erratum to CellML 1.1 (and indeed, such an erratum would be
> inappr
David Nickerson wrote:
> Andrew Miller wrote:
>
>> David Nickerson wrote:
>>
From what I gather, publicity. We need some way to direct people's
attention to our intention to deprecate reaction elements.
>>> sure - but its still not clear to me if 1.1.1 is m
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