Forums

Hello all,

if we check the units consistency of a model, there are basically
three possible outcomes:

A. the model can be proven to have correct units.
B. the model can be proven to be inconsistent (this means you cannot
determine the unspecified units in the mode so that it becomes
consistent).
C. the consistency cannot be determined (this means the unspecified
units could be choosen so that the model is consistent). Current sbml
assumes in this case that the model _is_ consistent.

What I think is important is this last point. A large number of models
fall in category C. We really should assume they have consistent
units. If we now allow case B as valid sbml models (units don´t have
to be consistent at all) it would be strange to assume consistency of
unspecified units.

Sven


Am 15.12.2007 um 04:06 schrieb Michael Hucka:

> The topic of this vote is:
> Should consistency of units be required?
>
> The URL for the voting page is:
> http://www.surveymonkey.com/s.aspx?sm=znse9ys51PMv5mMlma808w_3d_3d
>
> This survey ends 28 December 2007.
>
> The SBML Level 2 Version 3 Release 2 specification is at
> http://sbml.org/specifications/sbml-level-2/version-3/
>
> Section 4.10.4, 4.11.3, 4.11.4 and 4.14.4 (and corresponding
> validation rules) of the L2v3 specification currently state
> a requirement for the consistency of units of the left- and
> right-hand sides of mathematical expressions. The statement
> is that the units of measurement of the left- and right-hand
> sides *must* be equal. The specification is not explicit
> about how strictly this requirement is supposed to be
> interpreted. We suspect that many SBML developers and users
> assumed that the statements really meant the units only
> "*should*" be equal. We are therefore running this vote to
> determine how strict the SBML community prefers the
> requirement about unit consistency to be.
>
> The fundamental issue can be put as follows. Given two
> quantities A and B, with units of measurement given for
> both, should SBML specify that an expression
>
> A = B
>
> *must* have consistent units, or should it specify only
> that it *should* have consistent units? Put another
> way, if A and B have identical numerical values but
> different units, should SBML stipulate that the expression
> above be considered an invalid statement?
>
> Currently, the SBML specification makes it clear that pure
> numbers appearing in formulas (e.g., the "1" in an
> expression "A = B*1") and parameters have undefined units by
> default. (Parameters can be assigned units, but they have
> no default units defined.) This is not the same as being
> dimensionless. If a number or parameter without units
> appears in a formula, they may make it impossible to deduce
> the units of the overall expression. This is related,
> though not identical, to the present issue; in the present
> case, we are concerned with situations in which all the
> units are defined.
>
> Physically speaking, two quantities A and B are unequal
> if they have different units. However, in the domain of
> SBML, there are published models in the literature in which
> units were either deliberately or mistakenly not considered
> in the system of equations, resulting in inconsistent or
> impossible units. For example, in Ferreira AEN, Ponces
> Freire AMJ, and Voit EO, Biochem. J. 376:109-121, 2003
> (available as BioModels DB model #BIOMD0000000053), some of
> the rate laws given in table 1 have units of 1/(M*h) and
> others have M/h.
>
> The conundrum is that if SBML stipulates unit
> consistency is required for any and all valid SBML models,
> then these published models can't be represented in SBML,
> yet at the same time, such inconsistencies in a model could
> be argued to mean that the model contains errors (because
> A != B if units are taken into account).
>
> So what should SBML specify in this area? We would like
> your opinion on this matter. Please fill out the short
> survey at
>
> http://www.surveymonkey.com/s.aspx?sm=znse9ys51PMv5mMlma808w_3d_3d
>
> This survey ends 28 December 2007.
>
> Thanks,
> The SBML Editors
>
> ____________________________________________________________
> 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.