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Hi All, Here is my 2 cents worth on this subject.

I think the spec is pretty clear: The first line of section 4.7 is:

"A Parameter structure is used to declare a variable for use in
mathematical formulae in an SBML model definition."

http://www.sbml.org/specifications/sbml-level-2/version-1/html/sbml-
level-2.html#SECTION00047000000000000000

I don't think its necessary to have a separate section for
"constants" and "variables" because that could lead to confusion when
one wants to define a model that contains both constant and variable
rate constants.

I think the name "parameter" is ideal because it avoids specifically
calling anything either a "variable" or a "constant"; thats what the
"constant" field is for. I quote from dictionary.com:

pa·ram·e·ter  P Pronunciation Key (p-rm-tr)
n.
Mathematics.
A constant in an equation that varies in other equations of the same
general form, especially such a constant in the equation of a curve
or surface that can be varied to represent a family of curves or
surfaces.
One of a set of independent variables that express the coordinates of
a point.
One of a set of measurable factors, such as temperature and pressure,
that define a system and determine its behavior and are varied in an
experiment.
The word "parameter" as now used in SBML incorporates all of these
possible interpretations.

I don't think we should redefine things in SBML or add new fields
just because the name is confusing to some people who haven't read
the spec clearly.

I'm not going to make a big stink about this - I don't really care.
If people really want to change things I won't raise this argument
again.

BES


On Feb 9, 2006, at 11:51 PM, Herbert Sauro wrote:

>
> With the number of models growing in biomodels.net we are now able to
> see more variants of SBML than ever before. One thing that struck me
> today was model number 47 at biomodels.net, this has caused some
> problems for a number of simulators and was brought to my attention by
> some users.
>
> This model has a rateRule for a quantity called p3. However the
> rateRule
> is function of one of the species, it is therefore strictly a state
> variable just like a floating species. The trouble is, there is
> nowhere
> sensible to declare such a variable. It is obviously not a
> parameter and
> as some have noted, it is also not a species, so where should it go?
> Given that it is a state variable, and a rateRule at that, it should
> have an initial condition, so where does this go, into the list of
> global parameters? In fact, in the SBML p3 is initialized in the
> list of
> parameters even though it is not a parameter. Now I understand the
> confusion because where ever one puts it there would be disagreement.
>
> It would be convenient to have another section, called parhaps,
> listOfVariables (or something else) where one would list and
> initialize
> all those state variables that are not species, species would then be
> things that appear on the left and right hand sides of reactions.
>
> What does the community think?
>
> Herbert Sauro
>
> ----------------------------------------------------------------------
> --
> ---------
> Herbert M Sauro
> Assistant Professor
> Keck Graduate Institute
> 535 Watson Drive
> Claremont, CA, 91711
> Tel: 909 607 0377
> web site: www.sys-bio.org
>
> Trying to convice a believer of ID that ID isn't science is like
> trying
> to teach a pig to sing...it wastes your time and annoys the pig.