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Nicolas-

Sorry, I misunderstood what was current and what was proposed. This means
it's even more important to vote for SHOULD, not for MUST. I would urge
relaxation of the consistency rule for the reasons stated in my earlier
post.

RDP

-----Original Message-----
From: sbml-discuss-bounces@caltech.edu
[mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of Nicolas Le novère
Sent: Saturday, December 15, 2007 4:15 PM
To: SBML Discussion List
Subject: Re: [sbml-discuss] SBML survey: should consistency of unitsbe
required?

rphair@integrativebioinformatics.com wrote:
> But the current proposal to
> REQUIRE units consistency in a valid SBML model should be rejected.

Robert, this is not the current proposal. This is the current situation.
What we ask is if we keep things as they are or if we relax the
consistency rule.

> First, it is entirely possible to have different units in different parts
of
> a model. A simple example would be expressing cell surface receptor
binding
> using extracellular agonist concentrations and binding constants (Kd)
> expressed in mg/dl while all the intracellular concentrations are
expressed
> in Molar or nM. No inconsistency is created so long as the total binding
> capacity has units compatible with the rate laws in the second messenger
> signaling system model. This is true because the concentration of the
> extracellular signal and its Kd appear in the equilibrium binding
expression
> as a unitless ratio. I've made this point on multiple occasions, notably
in
> a long SBML-discuss thread on simple Michaelis-Menten rate laws, but the
> units police apparently have not been convinced.

That is perfectly fine. Such a model would not be rejected.

> It's a different story when you have A = B and the units on the two sides
> are inconsistent. It seems to me it would be far simpler for us assume
that
> when an equation appears in a SBML model, the parameters on the two sides
of
> the equal sign MUST have units that result in equality. If the STATED
> parameter units do NOT result in equality, the units are wrong. But you
> don't have to fix the units for the numerical solver to get the right
> answer. In some important sense, the solver knows what the units must be
and
> acts accordingly.

That is the current situation. Such a model would not only be judged as
being wrong and a WARNING issued, but the SBML itself would be declared
wrong and an ERROR issued.

--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: 468, Mob: +44(0)7833147074 Skype:n.lenovere
http://www.ebi.ac.uk/~lenov, AIM: nlenovere, MSN: nlenovere@hotmail.com
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