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Herbert's point is well taken and brings to mind another case that I'm not
clear how to encode in SBML.

Membrane potential (Vm). Clearly can be expected to change with time, but
just as clearly is not a Species. Some models obtain Vm by keeping track of
the charge on the membrane capacitance. This is then an algebraic rule
giving Vm = Q/C and the variation in time arises because the charged
species that make up Q are changing. In this case no initial condition is
required since the initial value of Vm is determined by the initial values
of the charged species. Other models write dVm/dt = i/C and the time
dependence arises from changing membrane currents that make up the total
current, i. In either case Vm is time varying, but in neither case is it
obvious to me how to encode it in SBML.

Other forces, such as osmotic pressure, hydrostatic pressure, tension
developed by contracting muscle, and even the Forces and fluxes of
non-equilibrium thermodynamics raise similar questions.

What is SBML best practice for such models? Do they imply a need for
Herbert's listOfVariables?

RDP

-----Original Message-----
From: sbml-discuss-bounces@caltech.edu
[mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of Herbert Sauro
Sent: Friday, February 10, 2006 2:52 AM
To: sbml-discuss@caltech.edu
Subject: [sbml-discuss] Suggestion for new section in SBML


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.