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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

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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.