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[cellml-discussion] Expanding the CellML abbreviation


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  • From: j.lawson at auckland.ac.nz (James Lawson)
  • Subject: [cellml-discussion] Expanding the CellML abbreviation
  • Date: Tue, 03 Jul 2007 15:06:38 +1200
Andrew Miller wrote:
> David Nickerson wrote:
>> Hi Andrew,
>>
>> Sounds like a good idea, although I would like to see the 'using
>> ordinary differential equations' bit dropped.
>>
> It was intended just to be an example, and I realise that CellML can be
> used for much more than just systems of ODEs. However, I think that the
> 'most commonly used to...' part is quite important, because although you
> could describe an economics problem using PDEs in CellML, this deviates
> both from the common usage and what any existing CellML tools (except
> perhaps JSim?) can deal with.

I think you're making the assumption here that people will necessarily
discriminate between what something is commonly used for and what it can
potentially be used for. We don't want to unwittingly pigeon-hole CellML
in the minds of the scientific public. Perhaps we should be touting
CellML's flexibility instead.

>
> Should the most common usage of CellML expand in the future, I see no
> reason why we couldn't expand it then. The problem I see with not
> including the information on how CellML is most commonly used in the
> example at this stage is that authors may try to qualify CellML in an
> incorrect way (which might imply that CellML can only be used for
> systems of ODEs, or can only be used for biological models), instead of
> using our exanple.
>> It would also be good to try and work this definition into the front
>> page at cellml.org - that is the most common place I look when I need a
>> brief blurb on CellML. Might possibly fit in with a new section on the
>> website on "How to cite CellML" ??
>>
> Referencing and citing CellML often occur together, so I think that this
> makes sense (although maybe "How to reference and/or cite CellML" would
> be a more accurate title?
>> Andre.
>>
>
> David Brooks wrote:
>> I certainly agree with your intent - more generally I feel is a need to
>> change people's interpretation of the abbreviation 'ML' from meaning
>> 'Markup Language' to meaning 'Modelling Language' - certainly "Cell
>> Modelling Language" is more accurate than "Cell Markup Language".
>
> The modelling part is more accurate, although the 'cell' part is still
> there, which I why I think it should simply be a name and not an
> abbreviation.
>
>> What
>> about "CellML (a mathematical modelling language most commonly used ...)"?
>>
> I think we want to make it clear it is a language primarily intended for
> the interchange of models between groups and / or tools, as opposed to
> say, MATLAB. Perhaps the word language is enough to imply this, but I'm
> not sure that this distinguishes something like MATLAB code, which is
> primarily used as an interface between a human and a computer, and a
> language specifically designed for interoperability and exchange (which
> the words markup language generally imply).
>
> Best regards,
> Andrew
>> -Dave
>>
>
>> Andrew Miller wrote:
>>
>>> Hi,
>>>
>>> I have noticed that a lot of people who refer to CellML (generally
>>> people who don't use CellML, but reference it) feel obliged to expand
>>> the abbreviation, and they generally expand it as "Cell Markup Language".
>>>
>>> As far as I am aware, we have never actually said that CellML stands for
>>> Cell Markup Language, and indeed, that expansion doesn't really make
>>> sense, because CellML does not aim to mark up cells at all, and it is in
>>> some sense independent of biology at a technical level. However, unless
>>> we can agree as a community that CellML doesn't stand for "Cell Markup
>>> Language", there is a risk that people will keep calling it that, which
>>> could result in a misunderstanding of what CellML is.
>>>
>>> I suggest that we put the following note up as an errata to the CellML
>>> specifications (please indicate whether you agree with the intention of
>>> this, and whether you agree with the specific wording):
>>>
>>> "CellML is not intended to be an abbreviation, but rather, it is simply
>>> a name used to identify the language. The fact that CellML starts with
>>> the word 'Cell' is a result of its original intended use. However,
>>> CellML is actually a generic mathematical modelling language which can
>>> be applied in a range of disciplines. It is worth noting that CellML
>>> does not stand for 'Cell Markup Language'. Instead, when introducing
>>> CellML to an audience who may be unfamiliar with it, a short explanation
>>> of CellML is recommended. For example, 'CellML (a mathematical model
>>> markup language most commonly used to describe biological systems using
>>> ordinary differential equations)' ".
>>>
>>> Best regards,
>>> Andrew
>>>
>>> _______________________________________________
>>> cellml-discussion mailing list
>>> cellml-discussion at cellml.org
>>> http://www.cellml.org/mailman/listinfo/cellml-discussion
>>>
>>
>
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