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Mike Hucka


Posts: 961
Registered:
October 2003
Re: What to do about his unit checking case 10 Feb '07 17:40 Go to previous messageGo to previous message

Dear Upi,

bhalla> Dear Mike, Did you consider the possibility of
bhalla>
bhalla> 1. defining a 'dimensionless' unit, and

Indeed, SBML already defines "dimensionless".

bhalla> 2. requiring that _every_ number have a unit
bhalla> attached, even if it is only 'dimensionless'?

Just as background, to clarify the situation (you may
already have this in mind; sorry if this is stating the
obvious), most fields taking numbers in SBML do have units
defined (along with defaults). Those units are associated
with the overall expression or overall value of the field.

The problem here involves numbers appearing within MathML
expressions, for example in reaction rate formulas. MathML
does not have a standard scheme for attaching unit and
dimensionality information to <cn>. There some suggestions,
e.g. at http://www.w3.org/TR/mathml-units/; they involve
using either <csymbol> or <semantics> and wrapping numbers
inside <apply></times>...</apply> to attach the unit
information. An alternative approach is taken in CellML,
where they allow the use of a "units" attribute in the
CellML namespace to be added to MathML <cn> elements, as in
for example

<math xmlns="http://www.w3.org/1998/Math/MathML">
....
<cn cellml:units="dimensionless"> -1.0 </cn>
...
</math>

Of the schemes I've seen, the CellML one is the simplest and
easiest. The MathML proposal at the URL mentioned above,
involving <semantics> or <csymbol>, results in much more
complicated expressions and probably a lot of opportunities
for errors.

It could be considered a failure of SBML that it does not
define a scheme for associating units with numbers.

Should such a facility be added?

MH

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SubjectPosterDate
Read Message   What to do about his unit checking case Mike Hucka08 Feb '07 18:11
Read Message   Re: What to do about his unit checking case Upinder Singh Bhalla08 Feb '07 18:22
Read Message   Re: What to do about his unit checking case  Mike Hucka10 Feb '07 17:40
Read Message   Re: What to do about his unit checking case Bill Denney09 Feb '07 06:48
Read Message   Re: What to do about his unit checking case Mike Hucka11 Feb '07 12:04
Read Message   Re: What to do about his unit checking case Darren J Wilkinson11 Feb '07 13:59
Read Message   Re: What to do about his unit checking case Stefan.Hoops12 Feb '07 08:55
Read Message   Re: What to do about his unit checking case Darren J Wilkinson12 Feb '07 11:08
Read Message   Re: What to do about his unit checking case Mike Hucka22 Feb '07 13:39
Read Message   Re: What to do about his unit checking case Nicolas Le Novere22 Feb '07 14:21
Read Message   Re: What to do about his unit checking case Mike Hucka22 Feb '07 14:53
Read Message   Re: What to do about his unit checking case Stefan.Hoops23 Feb '07 05:40
Read Message   Re: What to do about his unit checking case Mike Hucka23 Feb '07 11:24
Read Message   MathML help Tommaso Mazza01 Mar '07 08:58
Read Message   Re: MathML help Nicolas Le Novere01 Mar '07 14:10
Read Message   Re: MathML help Tommaso Mazza02 Mar '07 00:15
Read Message   Re: MathML help Mike Hucka02 Mar '07 14:39
Read Message   Re: MathML help Tommaso Mazza03 Mar '07 02:23
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