Forums

Hello all,

regarding the example: is there any meaning a rate law in 1/(M*h)
could have?

And Mike, you wrote that this specific model cannot be represented in
sbml. But could it not be written completely in dimensionless values
(dropping the inconsistent units, but keeping everything else)?

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



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I love units. I spend an inordinate amount of time trying to convince
experimentalists to pay more attention to units. But the current proposal to
REQUIRE units consistency in a valid SBML model should be rejected.

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.

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.

It is true that there are some apparent inconsistencies in the published
units in the Voit paper cited as an example of inconsistent units. But it
should be obvious that all the units in the published paper were added after
the hard modeling work was completed. Solvers don't track units.

Has anyone had the courtesy to write to Eberhard asking him to comment on
the units? To me, these apparent unit inconsistencies simply demonstrate
that the stated units are wrong either because of a publisher's or printer's
error or an oversight. But the model accounts for the data and, really, only
the numerical values of the parameters are relevant to the numerical
solutions.

Something would be deeply wrong with SBML if it forced us to exclude the
Voit model because the units police claim it says A = B when A and B have
different units even though it is obvious that the numerical integration has
no need of units and the numerical solution is clearly internally consistent
and accounts for the data.

Vote SHOULD, not MUST!

RDP

PS As an aside, it should be clear that if you are importing a parameter
value into your model that was measured by someone else in some related
experiment, then you MUST convert that parameter to the units used in your
model before you enter it in your SBML file. Naturally, this conversion
will, in general, change its numerical value.

-----Original Message-----
From: sbml-discuss-bounces@caltech.edu
[mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of Michael Hucka
Sent: Friday, December 14, 2007 7:07 PM
To: sbml-discuss@caltech.edu
Subject: [sbml-discuss] SBML survey: should consistency of units be
required?

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
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http://sbml.org/forums/

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



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Hugh,

Although I think you are right this would often be the case, this is not
obligatory. The conversion between units could occur within parameters
(think about the specific enzyme activity ...)

hugh.d.spence@gsk.com wrote:
>
> Mike
> Models using x umole of amino acids + y umole of glucose + z
> umole Ca2+ to produce 1 g of biomass can't have consistency of units.
> It was for these models that we introduced mass units in the
> first place.
> The proposal is equivalent to removing the mass units from SBML.
>
>
>
> Hugh Spence
> GSK Scientific Computing and Mathematical Modelling
> Medicines Research Centre
> Gunnels Wood Road
> Stevenage
> UK
> SG1 2NY
>
>
>
>
>
> *"Michael Hucka" <mhucka@caltech.edu>*
> Sent by: sbml-discuss-bounces@caltech.edu
>
> 15-Dec-2007 03:06
> Please respond to "SBML Discussion List" <sbml-discuss@caltech.edu>
>
>
>
> To
> sbml-discuss@caltech.edu
> cc
>
> Subject
> [sbml-discuss] SBML survey: should consistency of units be required?
>
>
>
>
>
>
>
>
> 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.
>
>
> -----------------------------------------------------------
> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
> -----------------------------------------------------------
>
>
> ------------------------------------------------------------------------
>
> ____________________________________________________________
> 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.


--
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
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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
____________________________________________________________
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
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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.



____________________________________________________________
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https://utils.its.caltech.edu/mailman/listinfo/sbml-discuss

For a web interface to the sbml-discuss mailing list, visit
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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
> ____________________________________________________________
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>
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>
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> contact sbml-team@caltech.edu.
>
>
>
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> <
> winmail
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Dr. Sven Sahle
Abteilung Modellierung biologischer Prozesse
Universität Heidelberg, BIOQUANT/Zoologie



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Dear Sven and all,

Dear Jordan and all,


Am 16.12.2007 um 19:50 schrieb Jordan Atlas:

>
> Dear Sven and all,
>
>> 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).
>
>
> I don't know the background for the model merging efforts, but do
> all models need to be "mergable"? If not, then requiring units be
> consistent (in ALL models) so that models can be merged seems
> unnecessary.

No, models don´t have to be "mergable". But I think if we take the
effort to do units one of the things that should be possible with it
is to convert units; e.g. if you have a model in mmol it should be
possible to convert it to mol with a suitable tool. I think this is
only possible if the tools knows that the units are consistent.

>> 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)
>
>
> If there are cases when a tool cannot find out if the units are
> consistent, then how is it possible to enforce consistency (i.e.
> SHOULD)?

E.g., consider you have an assignment rule a = b*c, where the units
of a and b are known and c is a global parameter with a given value
but unspecified units. A tool could now figure out what the units of
c needs to be, so the model could be converted to a different set of
units, possibly changing the numerical value of c to match the new
units. But this is only possible if we can rely on the units to be
consistent.
If we do not require that the units are consistent, the tool has no
way to find out about the units of c.

I really do not see the need to be able to specify inconsistent
units. Having a model with inconsistent units would say: "I have a
model which gives the right results numerically. However, I do not
want to get the units right, please don´t rely on them." For this
case, I think, one could use unspecified or dimensionless units,
without the need to relax the requirements of the sbml specification.

Sven

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



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>

Hello Sven and all

> I really do not see the need to be able to specify inconsistent
> units. Having a model with inconsistent units would say: "I have a
> model which gives the right results numerically. However, I do not
> want to get the units right, please don´t rely on them." For this
> case, I think, one could use unspecified or dimensionless units,
> without the need to relax the requirements of the sbml specification.
>

prefering strict units my self, and agreeing wholeheartedly with what
you said above, there is another side to this. No one would come along
with a mindset of "I do not want to get the units right, please don´t
rely on them.". Rather the issue is one of model exchangeability
between software tools. Until now we could pretty much exchange SBML
models freely between tools, even though the units might have been
inconsistent. With libSBML giving us the ability to flag these
inconsistencies as warnings, that was fine as well. Now however, if
every inconsistency is treated as Error (as the spec prescribes), the
problem will be that we loose a whole lot of exchangeability, between
'strict' tools and more forgiving ones.

Modelers that have been using tools for years, with kinetic formulas
that were "modellingly correct" albeit inconsistent unit-wise, would
be hard pressed to understand, why they couldn't exchange their models
like they did before.

Going forward, and working on model-modularity ourselves, I think the
right step to take is to make it known to the community at large that
starting from a specific SBML level/version, units will be interpreted
by the tools as 'strict', and will be rejected otherwise. This would
allow tools to gracefully treat SBML files of prior versions as
'conceptual' models in case of unit-inconsistencies, but i guess that
would be a 'tool issue' :).

best
Frank
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Sven Sahle wrote:

> I really do not see the need to be able to specify inconsistent
> units. Having a model with inconsistent units would say: "I have a
> model which gives the right results numerically. However, I do not
> want to get the units right, please don´t rely on them." For this
> case, I think, one could use unspecified or dimensionless units,
> without the need to relax the requirements of the sbml specification.

Not always. The problem is that you may not want, or be able, to specify
a unit as unspecified for the whole model. And a merging process could
actually lead to that. A parameter could need to be unspecified to
forbid consistency check on a weird math expression, such as:

[X] = k * [Y]^p1

(To cut any discussion on the relevance of that expression, let's say it
comes from an empirical curve-fitting procedure). If we say p1 has
undefined units, there is no problem.

Now, let's imagine we merge this model with another one where a
parameter p2 represents the same concept, and p2 has a defined unit. And
for some reason, the merging process decides that the p to keep in the
resulting model is p2 (for instance because it results from a process
and is no longer a constant), what do-we do? Should-we remove all the
units? Is-the choice between full consistency or no unit at all?

As a modeller I would tend to think that some information is better than
nothing.


--
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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Hello All,

I have been quiet on this thread which does not mean that I do not
care :) You all know my background is physics and therefore for me
all values have units and all units in formulas must be consistent to
make any sense.

However the current situation in SBML is that parameters have the
default unit "undefined" (not that this a unit ;). In addition any
numbers appearing in MathML also have the unit "undefined. The first
issue can be easily overcome by a modeler by specifying the correct
units for any parameter. This way one can also convert between grams and
mole if the model requires it within any mathematical formula by
introducing a conversion parameter.

The second is a far greater problem. Basically, any expression using a
number can not be verified to have correct units. To overcome this any
number used in an expression must be defined as a parameter with the
unit dimensionless and this parameter must be used instead.

The above means it is currently possible to define models in SBML,
which have consistent units and these can also be verified. But to
define such a model is extremely cumbersome and lets face is it nobody
is doing it.

This means if we want that units MUST match we need to make things
easier in SBML. The first thing would be to require that parameters
have the default units dimensionless and that numbers are also
dimensionless. In addition the unit "undefined" must be removed.

If we do all this, MUST match is clearly the right way to go. This would
mean that we can not use all models as they currently appear in
publication instead they need to be curated so that the units
match. This means introducing parameters with the value 1 and the
proper units wherever needed. This is what the authors did without
thinking about it anyway ;)

But of course this vote is not about getting rid of the unit
"undefined". It is about what can we do in the current situation. We
can use MUST match or we can use SHOULD match. SBML as it stands now is
clearly geared towards SHOULD as its unit system is as closed to broken
as it gets. Let me consider the two expressions where A and B have
inconsistent units

a) 1 = A/B
b) A = B.

The first one can not be verified to have correct units and a warning
is given. It is not flagged as an error and therefore the SBML
is valid. The second is easily verified to have incorrect units and
therefore if we go with MUST is invalid SBML. On the other hand if we go
with SHOULD a warning will be given and the result is again valid SBML.

Since both expressions say the same the result should be the same,
i.e., in the current context a SHOULD match leads to a more consistent
interpretation of the mathematical expressions in SBML.

I know this was long but I hope you are still reading :)

Thanks,
Stefan


On Sun, 16 Dec 2007 14:36:24 -0800
Frank Bergmann <fbergman@u.washington.edu> wrote:

> >
>
> Hello Sven and all
>
> > I really do not see the need to be able to specify inconsistent
> > units. Having a model with inconsistent units would say: "I have a
> > model which gives the right results numerically. However, I do not
> > want to get the units right, please don´t rely on them." For this
> > case, I think, one could use unspecified or dimensionless units,
> > without the need to relax the requirements of the sbml
> > specification.
> >
>
> prefering strict units my self, and agreeing wholeheartedly with
> what you said above, there is another side to this. No one would come
> along with a mindset of "I do not want to get the units right,
> please don´t rely on them.". Rather the issue is one of model
> exchangeability between software tools. Until now we could pretty
> much exchange SBML models freely between tools, even though the units
> might have been inconsistent. With libSBML giving us the ability to
> flag these inconsistencies as warnings, that was fine as well. Now
> however, if every inconsistency is treated as Error (as the spec
> prescribes), the problem will be that we loose a whole lot of
> exchangeability, between 'strict' tools and more forgiving ones.
>
> Modelers that have been using tools for years, with kinetic formulas
> that were "modellingly correct" albeit inconsistent unit-wise, would
> be hard pressed to understand, why they couldn't exchange their
> models like they did before.
>
> Going forward, and working on model-modularity ourselves, I think
> the right step to take is to make it known to the community at large
> that starting from a specific SBML level/version, units will be
> interpreted by the tools as 'strict', and will be rejected otherwise.
> This would allow tools to gracefully treat SBML files of prior
> versions as 'conceptual' models in case of unit-inconsistencies, but
> i guess that would be a 'tool issue' :).
>
> best
> Frank
> ____________________________________________________________
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>
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> contact sbml-team@caltech.edu.


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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Hello Nicolas,

I think you are missing my point. I said if we want to enforce
units, i.e., say MUST match, than we need to go all the way. This in my
opinion means getting rid of the dimension "undefined". However we have
decided not to go all the way and therefore we can only say SHOULD
match.

On Mon, 17 Dec 2007 22:39:07 +0000
Nicolas Le novère <lenov@ebi.ac.uk> wrote:

> Stefan Hoops wrote:
>
> > This means if we want that units MUST match we need to make things
> > easier in SBML. The first thing would be to require that parameters
> > have the default units dimensionless and that numbers are also
> > dimensionless. In addition the unit "undefined" must be removed.
> >
> > If we do all this, MUST match is clearly the right way to go. This
> > would mean that we can not use all models as they currently appear
> > in publication instead they need to be curated so that the units
> > match. This means introducing parameters with the value 1 and the
> > proper units wherever needed. This is what the authors did without
> > thinking about it anyway ;)
>
> No, no. We discussed that in length and in great details at the
> Hackathon. Numbers cannot be always dimentionless. What about an
> Hill-like function (something used a fair amount of time by the
> community of modeller, so we cannot dismiss it):
>
> [X]^n / ( 1 + [X]^n)
>
> 1 cannot be dimensionless if [X] is not dimensionless.
>

Yes, and making the units of 1 undefined an letting the user or tool
guess does not make it better.

> And please, everybody, don't ask me to write:
>
>
> ([X]/p)^n / ( 1 + ([X]/p)^n)
>
> with p = 1 M ...

I guess in the interest of proper unit definitions and checking rules,
I would like to ask you to write:

[X]^n / ( p^n + [X]^n)

But of course we have decided against that ;)

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility I
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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The topic of this vote was:
Should consistency of units be required?

Thank you all for your participation in the SBML electronic
vote on this issue. The voting on this topic is closed.
For reference, the call for votes can be found at this URL:
http://www.surveymonkey.com/s.aspx?sm=znse9ys51PMv5mMlma808w_3d_3d

This survey brought 20 unique votes. The results were
distributed as follows:

Case of "must": prefer requiring unit consistency: 4
Case of "should": prefer recommending consistency: 15
No opinion: 1
-----------
Total votes: 20

A large number of people included comments with their survey
responses. The following are the comments, in no particular
order, and with author names withheld for anonymity:

Comment How the person voted
------- --------------------
"The authors should be responsible "should"
for their models and SBML should
not micromanage."

"For any XML document there is "should"
'well-formed' (xml syntax) and
'valid' (schema syntax). SBML also
has 'validation rules' (document
semantics via libSBML) and 'MIRIAM'
(overall quality standards for the
encoded model via curators). For
purely practical reasons, unit
consistency is a model
quality/MIRIAM issue."

"This was the most interesting "should"
discussion of recent times!"

"Unit checking should be a service "should"
offered to modellers and reviewers
by SBML-associated software
(e.g. libSBML). It is the
responsibility of the modeller to
get their models right. Placing the
responsibility somewhere else is
asking for trouble."

"After the recent Phair thread, "should"
I'll be surprised at any 'MUST'
votes."

"Consistent units CAN NOT be used "should"
for a model where biomass is on one
side of the equation. (35 uMole
Amino acid + 50 uMole glucose + 10
uMole NH4OH = 1 g biomass)."

"Choosing the "SHOULD" option still "should"
allows the toolmakers to check for
unit consistency. If a particular
application requires consistent
units, the tool in question can
check for it and return an error if
there is inconsistency. If the
'MUST' option is selected, there is
a risk that some tools will support
unit checking (and therefore 'real'
SBML), while others will not.
Furthermore, if the 'MUST' option
is selected, I suspect it would
encourage some modelers to just
remove units from their models all
together in order to more rapidly
satisfy the requirement. Without
the consistency requirement, the
units might still be useful for
output display, etc. Finally, I'm
not aware of whether the
specification covers this, but how
does SBML treat quantities such as
the logarithm of a unit? For
example, if I have a species 'A',
and a parameter 'logA', which is
defined as 'logA' = log(A) (by
assignment), will it be possible to
satisfy the unit consistency
constraint? Or would one have to
define the rule as 'logA' =
log(A/units(A))?"

"I could go either way on this "no opinion"
vote. Perhaps a gray scale metric
of model validity would be better,
e.g. call the Ferreira model valid
but label it with a warning about
its units."

"Since we have units they must be "must"
correct otherwise it is an
error. As you pointed out,
incorrect units can always be made
correct if you multiply by 1."

"In my opinion ... even models, "should"
that don't have units defined can
exhibit rather interesting
behavior. By restricting ourself
to allow only for models with
consistently defined I think we
might loose a substantial part of
the SBML user base. That is not to
say, that if units are defined, and
they clash, this should be flagged
as an error. This means however
also, that there should be no
default units on
compartments/species ... The model
you mention above seems to define
exactly one unit to be used in the
model (i.e. hour). Oh ... and let
us not forget all the models that
are .. "modellingly correct", as it
were ... I think we have to keep
them around, so as not to alienate
more people."

"I think it's stupid that A = B "should"
would be considered true even if
the units weren't compatible, but
if we can't represent some
published models as a result, then
we don't seem to have much choice."


Thank you again for taking the time to respond to the survey
and for the very interesting discussions that took place on
sbml-discuss.

Best regards,
Mike (on behalf of the SBML Editors)

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