Forums

Hello all,

regarding work in progress, on one hand there is nothing stopping you
from exchanging invalid sbml files if you edit them manually. On the
other hand, if you use tools to create the sbml files, the tool should
make sure that the units are consistent even for half finished models.
As far as I understand units this is always possible.

I think we urgently need to figure out what the units are supposed to
do. If we consider units just as some informal annotation to the
model we are free to decide whether we want to require consistency.
Then the units would be useful more or less for display and
documentation purposes only.

On the other hand I think the main benefit of units is that if units
are known we can write tools that convert units, which is _needed_ for
model merging. And this is only really possible if the units are
correct. (And correct units are possible even for all these difficult
cases involving mass units)

So I personally (as you may know) dislike the units in sbml, but if
they are to be useful they need to be consistent (MUST). If we do not
require this (SHOULD) we should add a flag to the model to indicate if
the units are to be considered consistent, so that a tool can know if
operations working with units are possible. (This is necessary because
there are cases when a tool cannot find out if the units are
consistent or not)

Sven



Am 16.12.2007 um 07:02 schrieb Schaff,Jim:

> Robert, Michael, Nicholas, Sven,
>
> Although I may be considered part of the "unit police", I agree that
> unit consistency should not be tied to SBML document validity. My
> main reason is that sbml should allow exchange of "works in
> progress" between tools (not yet having consistent units), not just
> for final, curated publication.
>
> I would suggest that MIRIAM or BioModels.net mandate that curators
> find a way to properly reconcile units in the spirit of the paper/
> model, else strip them to dimensionless as Sven suggested.
>
> Jim Schaff
> Virtual Cell Project (vcell.org)
>
>
> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu on behalf of rphair@integrativebioinformatics.com
> Sent: Sat 12/15/2007 7:59 PM
> To: 'SBML Discussion List'
> Subject: Re: [sbml-discuss] SBML survey: should consistency
> ofunitsbe required?
>
> 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
> ____________________________________________________________
> To manage your sbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss
>
> For a web interface to the sbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the sbml-discuss list,
> contact sbml-team@caltech.edu.
>
>
>
> ____________________________________________________________
> To manage your sbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss
>
> For a web interface to the sbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the sbml-discuss list,
> contact sbml-team@caltech.edu.
>
> <
> winmail
> .dat>____________________________________________________________
> To manage your sbml-discuss list subscription, visit
> https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss
>
> For a web interface to the sbml-discuss mailing list, visit
> http://sbml.org/forums/
>
> For questions or feedback about the sbml-discuss list,
> contact sbml-team@caltech.edu.

Dr. Sven Sahle
Abteilung Modellierung biologischer Prozesse
Universität Heidelberg, BIOQUANT/Zoologie



____________________________________________________________
To manage your sbml-discuss list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
http://sbml.org/forums/

For questions or feedback about the sbml-discuss list,
contact sbml-team@caltech.edu.