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Posts: 961
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October 2003
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Posts: 96
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September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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16 Jan '06 09:06
 
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Hello All,
This vote is what I have been afraid of from the beginning of the whole
sboTerm discussion. We had agreed that the Math element is authoritative
and now it shall become optional. Can anybody explain to me how an
optional field can be authoritative?
This is in my opinion an attempt through the back door to make the
sboTerm authoritative by just omitting the Math element in the kinetic
law. Mike actually states this in his pro argument. I have expected this
but not this fast. We do not have sboTerms and we do not have any tools
understanding them. I think we should wait with this at least until we
have some experience with both of them, as Sven had suggested earlier in
this list. I really mean both since without tools using the sboTerms
they are still 'worthless'.
But let me come to the other pro optional argument given by Mike. The
kinetic law itself is optional, i.e., we already have the ability to
store models which are not 'fully fleshed out'. Since we know already
the list of substrates, products and modifiers, from the reaction
element there is no benefit in writing an 'empty' kinetic law without a
mathematical expression. Because it is this expression is which allows
us to define and give meaning to to kinetic parameters.
In addition I think it is not a good approach to allow for two ways to
specify the same. This will eventually open up ambiguity, which we are
fighting anyway.
Thanks,
Stefan
On Fri, 13 Jan 2006 16:15:44 -0800
Michael Hucka <mhucka@caltech.edu> wrote:
> The topic of this vote is:
> MAKING 'MATH' OPTIONAL IN KINETICLAW
>
> The URL for the voting page is:
> http://www.surveymonkey.com/s.asp?u=211621674447
>
> Additional background is available in the minutes from the
> October SBML Forum meeting at
> http://www.sbml.org/forums/index.php?t=msg&th=713&rid=2
>
> The draft SBML Level 2 Version 2 Specification is at:
> http://sbml.org/wiki/sbml-level-2-version-2.pdf
>
>
> The field 'math' in KineticLaw is today a required field
> (though the KineticLaw itself is optional in a Reaction).
> Should 'math' be made optional?
>
> There are at least two arguments for making 'math' optional.
> One is that it allows more flexibility in model creation and
> development, for example by making it possible to store and
> read models having parts that are not fully fleshed out.
> Even though such models can't be properly simulated, they
> may still have some utility to the modelers creating them.
> A second argument arose recently in the context of proposals
> to add 'sboTerm', a field for referring to controlled
> vocabulary terms. Making 'math' option would allow
> partially-defined models where some reactions specified
> using just the 'sboTerm' references. To make this possible,
> kinetic laws without 'math' should be introduced. (However,
> there is also general agreement that models without a 'math'
> field on a kinetic law would be considered uncharacterized
> in the same way as, for example, a model without a kinetic
> law, or with missing initial values.)
>
> The principal argument against making 'math' optional is the
> belief that the proper granularity should be at the whole
> KineticLaw object level. This encourages greater
> completeness in model creation, by removing the possibility
> of creating models containing kinetic laws where (for
> example) only local parameters are given in a reaction but
> no actual mathematical expression in which they're supposed
> to go.
>
> Please cast your vote by using the voting page at
> http://www.surveymonkey.com/s.asp?u=211621674447
>
> Mike and Andrew
--
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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Posts: 469
Registered:
October 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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16 Jan '06 11:57
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> This is in my opinion an attempt through the back door to make the
> sboTerm authoritative by just omitting the Math element in the kinetic
> law.
No, it is not. It is an issue independant of sboTerm. It is larger than that.
> But let me come to the other pro optional argument given by Mike. The
> kinetic law itself is optional, i.e., we already have the ability to
> store models which are not 'fully fleshed out'. Since we know already
> the list of substrates, products and modifiers, from the reaction
> element
But not the local parameters! So far SBML has been tied to ODE-type
models. But there is an increasing pressure to make it accept other kind
of models.
The ability to store local parameters without a kineticLaw is a desirable
feature for some quantitative descriptions that are not kinetics models
per se (particularly if the parameters are properly annotated ...).
SBML is the Systems Biology Markup Language, not ODE-ML. It was very
clever to restrict its use to one kind of model initially. It was
certainly seminal in its adoption. But it is a fact that SBML is now used
by a much wider community.
In the current situation, the user has the choice between a representaiton
that one can instantiate in a time-serie simulation (with kineticLaw), and
a completely qualitative representation (without kineticLaw). There is
maybe a middle-way.
We are not advocating for a wild explosion of SBML elements here. But on
the contrary for simpler SBML models. Even COPASI could read such models,
even it they would be undetermined. A user would have to complete them to
run simulations. But this is already the case if he/she import a model
from Reactome or KEGG.
The problem is that an empty MathML returns "0". It is not undefined. One
can decide that the following return "0"
<math>
<apply>
</apply>
</math>
while <math /> returns undefined.
--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov
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Posts: 96
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September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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17 Jan '06 06:29
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Hello Nicholas,
On Mon, 16 Jan 2006 19:58:34 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:
>
> > This is in my opinion an attempt through the back door to make the
> > sboTerm authoritative by just omitting the Math element in the
> > kinetic law.
>
> No, it is not. It is an issue independant of sboTerm. It is larger
> than that.
>
> > But let me come to the other pro optional argument given by Mike.
> > The kinetic law itself is optional, i.e., we already have the
> > ability to store models which are not 'fully fleshed out'. Since we
> > know already the list of substrates, products and modifiers, from
> > the reaction element
>
> But not the local parameters! So far SBML has been tied to ODE-type
> models. But there is an increasing pressure to make it accept other
> kind of models.
> The ability to store local parameters without a kineticLaw is a
> desirable feature for some quantitative descriptions that are not
> kinetics models per se (particularly if the parameters are properly
> annotated ...).
Any kind of local parameter is associated with a mathematical
expression, be it for 'traditional ODE' modelling, stochastic
modelling, or flux balance analysis. These kinetics can be expressed in
MathML omitting it is not the solution. To overcome the current
restrictions I would suggest kinetic laws for different kind of
modelling, i.e. subtyping. This would also allow two supposedly similar
models to be expressed in one SBML file, e.g. a stochastic model and an
ODE model. Results could than easily obtained from two different types
of integration. I am definitely opposed to removing the contents from
the SBML and putting it in the annotation like the sboTerm. The model
must be interpretable without it the annotation (sboTerm) provides the
context.
>
> SBML is the Systems Biology Markup Language, not ODE-ML. It was very
> clever to restrict its use to one kind of model initially. It was
> certainly seminal in its adoption. But it is a fact that SBML is now
> used by a much wider community.
>
You are absolutely correct. But as I said removing the contents from the
SBML and putting it in an sboTerm can not be the solution.
> In the current situation, the user has the choice between a
> representaiton that one can instantiate in a time-serie simulation
> (with kineticLaw), and a completely qualitative representation
> (without kineticLaw). There is maybe a middle-way.
Yes, as I suggested above. I think we are jumping the gun I am
definitely for enhancing the capabilities of the kinetic law. But
currently this is not even discussed. I think there are more consistent
solutions which will leave the contents in SBML.
>
> We are not advocating for a wild explosion of SBML elements here. But
> on the contrary for simpler SBML models. Even COPASI could read such
> models, even it they would be undetermined. A user would have to
> complete them to run simulations. But this is already the case if
> he/she import a model from Reactome or KEGG.
>
> The problem is that an empty MathML returns "0". It is not undefined.
> One can decide that the following return "0"
>
> <math>
> <apply>
> </apply>
> </math>
>
> while <math /> returns undefined.
I do not see the problem as you correctly pointed out the math lement
can return undefined :)
Let me make one thing clear at the end, I am not against sboTerms.
Actually, I am very much in favor of a controlled vocabulary. The only
problem is that the contents of the SBML file is shifted to the
controlled vocabulary. In the extreme this means we I just would need an
Biomodels ID and no SBML at all:)
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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Posts: 469
Registered:
October 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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17 Jan '06 09:04
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On Tue, 17 Jan 2006, Stefan Hoops wrote:
>> The ability to store local parameters without a kineticLaw is a
>> desirable feature for some quantitative descriptions that are not
>> kinetics models per se (particularly if the parameters are properly
>> annotated ...).
>
> Any kind of local parameter is associated with a mathematical
> expression, be it for 'traditional ODE' modelling, stochastic
> modelling, or flux balance analysis.
I'm not sure for logical modelling or petri net. Also, you can
describe an equilibrium with a Kd, without developping into a
reversible mass-action law. If you know the Kd, you can use a rapid
equilibrium in StochSim. You do not need the kon and koff. But if you
need to represent the reaction velocities, you need to.
> I am definitely opposed to removing the contents from
> the SBML and putting it in the annotation like the sboTerm. The model
> must be interpretable without it the annotation (sboTerm) provides the
> context.
But that is not already not entirely true. To take my usual example,
(Vmax * S) / (Km + S)
Can represent
S+E -> SE -> E+P
S+E <=> SE -> E+P with S+E <=> SE a rapid equilibrium
S+E <=> SE -> E+P with SE in steady-state
You can't tell. And this is what SBO is about. Adding meaning. But
that is NOT the topic of the current discussion. I know you do not
believe me, but I swear. This topics is independant of SBO.
--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov AIM screen name: nlenovere
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Posts: 23
Registered:
November 2005
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Posts: 96
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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18 Jan '06 07:21
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Hello Nicholas,
On Tue, 17 Jan 2006 17:04:02 +0000 (GMT)
Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> On Tue, 17 Jan 2006, Stefan Hoops wrote:
>
> >> The ability to store local parameters without a kineticLaw is a
> >> desirable feature for some quantitative descriptions that are not
> >> kinetics models per se (particularly if the parameters are properly
> >> annotated ...).
> >
> > Any kind of local parameter is associated with a mathematical
> > expression, be it for 'traditional ODE' modelling, stochastic
> > modelling, or flux balance analysis.
>
> I'm not sure for logical modelling or petri net. Also, you can
I am not sure either but not being sure is bad reason either way :).
> describe an equilibrium with a Kd, without developping into a
> reversible mass-action law. If you know the Kd, you can use a rapid
> equilibrium in StochSim. You do not need the kon and koff. But if you
> need to represent the reaction velocities, you need to.
In StochSim you have an underlying set of assumption and rules, i.e.,
mathematical expressions or functions. For anyone to understand how your
tool interprets the model you need to phrase that in the Math element.
It is probably not a rate law instead it is an algebraic expression
something like SE = kd * E. You should not do that via sboTerms as this
removes the contents from SBML. In anyway, "Mathematics" is considered a
rich universal language and that is why we agreed to use it in SBML to
begin with.
>
> > I am definitely opposed to removing the contents from
> > the SBML and putting it in the annotation like the sboTerm. The
> > model must be interpretable without it the annotation (sboTerm)
> > provides the context.
>
> But that is not already not entirely true. To take my usual example,
>
> (Vmax * S) / (Km + S)
>
> Can represent
>
> S+E -> SE -> E+P
>
> S+E <=> SE -> E+P with S+E <=> SE a rapid equilibrium
>
> S+E <=> SE -> E+P with SE in steady-state
>
> You can't tell. And this is what SBO is about. Adding meaning. But
> that is NOT the topic of the current discussion. I know you do not
> believe me, but I swear. This topics is independant of SBO.
You are right from the mathematical expression I do not know how the
kinetics was derived. The model is mathematically interpretable without
that knowledge. The addition of sboTerm will tell you how the Math was
derived and what other assumption you are making in the model. It is
obvious that we may have multiple sboTerms annotating the the same Math
element and that is exactly what we want.
Just one last question by making the Math element optional and
providing content through sboTerm we make SBML depend on SBO. Is that
the correct approach?
Thanks,
Stefan
>
> --
> Nicolas LE NOVERE, Computational Neurobiology,
> EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD,
> UK Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob:
> +33(0)689218676 http://www.ebi.ac.uk/~lenov AIM
> screen name: nlenovere
--
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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Posts: 469
Registered:
October 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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18 Jan '06 13:22
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>> describe an equilibrium with a Kd, without developping into a
>> reversible mass-action law. If you know the Kd, you can use a rapid
>> equilibrium in StochSim. You do not need the kon and koff. But if you
>> need to represent the reaction velocities, you need to.
>
> In StochSim you have an underlying set of assumption and rules, i.e.,
> mathematical expressions or functions. For anyone to understand how your
> tool interprets the model you need to phrase that in the Math element.
> It is probably not a rate law instead it is an algebraic expression
> something like SE = kd * E.
You are right with that example.
> You should not do that via sboTerms as this
> removes the contents from SBML.
I'm bewildered. How comes SBO sneaked in here again. What is the relevance?
> In anyway, "Mathematics" is considered a
> rich universal language and that is why we agreed to use it in SBML to
> begin with.
But the math element of kineticLaw is not any mathematical expression. It
is a mathematical expression describing the velocity of a reaction in
substance/tiem units.
--
Nicolas LE NOVÈRE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov
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Posts: 961
Registered:
October 2003
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Posts: 96
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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19 Jan '06 07:03
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Hello Nicholas,
On Wed, 18 Jan 2006 21:22:55 +0000 (GMT)
Nicolas Le Novère <lenov@ebi.ac.uk> wrote:
>
> >
> > In StochSim you have an underlying set of assumption and rules,
> > i.e., mathematical expressions or functions. For anyone to
> > understand how your tool interprets the model you need to phrase
> > that in the Math element. It is probably not a rate law instead it
> > is an algebraic expression something like SE = kd * E.
>
> You are right with that example.
>
> > You should not do that via sboTerms as this
> > removes the contents from SBML.
>
> I'm bewildered. How comes SBO sneaked in here again. What is the
> relevance?
I get your point :)
>
> > In anyway, "Mathematics" is considered a
> > rich universal language and that is why we agreed to use it in SBML
> > to begin with.
>
> But the math element of kineticLaw is not any mathematical expression.
> It is a mathematical expression describing the velocity of a reaction
> in substance/tiem units.
You are exactly right, this is exactly why I suggest subclassing of
the kinetic law to be able to describe other mechanisms than ODE in an
earlier message in the is thread :)
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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Posts: 73
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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19 Jan '06 13:28
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--- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > Any kind of local parameter is associated with a
> mathematical
> > > expression, be it for 'traditional ODE' modelling,
> stochastic
> > > modelling, or flux balance analysis.
> >
> > I'm not sure for logical modelling or petri net. Also, you
> can
>
> I am not sure either but not being sure is bad reason either
> way :).
Clearly you both need to read my book! ;-)
I'm certainly not aware of any modelling framework where a rate
parameter makes sense completely independently of any rate law.
There are frameworks where rates and rate laws are not used at
all, but then kinetic laws are not required, so we are all
happy. There are also frameworks where there is a
_default_assumption_ about the nature of the rate law (such as
for stochastic petri nets and discrete stochastic modelling more
generally) - namely that unless otherwise stated, irreversible
mass-action stochastic kinetics is assumed. But in this case it
is clear what the rate law is, so there is no problem for tools
to include it when they write the SBML, and there is nothing to
stop tools from ignoring it when they read it. So I must admit
that I am a bit puzzled as to why it is such a big deal to make
the math optional. What is the harm in including it for
completeness?
Yours,
--
Darren Wilkinson
email: darrenjwilkinson@btinternet.com
home www: http://www.darrenjwilkinson.btinternet.co.uk/
work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
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Posts: 349
Registered:
September 2003
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RE: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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23 Jan '06 15:35
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There are a whole range of models which do not depend on rate laws,
probably the most ell know begin flux balance analysis, but others exist
to. However, SBML databasea such as biomodels.net do not consider these
to be valuable models and will not accept them into the database. So
perhaps rate law free models in SBML should not be permitted althohgh I
think otherwise.
Herbert Sauro
-----Original Message-----
From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
Sent: Thursday, January 19, 2006 1:28 PM
To: SBML Discussion List
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw
--- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > Any kind of local parameter is associated with a
> mathematical
> > > expression, be it for 'traditional ODE' modelling,
> stochastic
> > > modelling, or flux balance analysis.
> >
> > I'm not sure for logical modelling or petri net. Also, you
> can
>
> I am not sure either but not being sure is bad reason either way :).
Clearly you both need to read my book! ;-)
I'm certainly not aware of any modelling framework where a rate
parameter makes sense completely independently of any rate law.
There are frameworks where rates and rate laws are not used at all, but
then kinetic laws are not required, so we are all happy. There are also
frameworks where there is a _default_assumption_ about the nature of the
rate law (such as for stochastic petri nets and discrete stochastic
modelling more
generally) - namely that unless otherwise stated, irreversible
mass-action stochastic kinetics is assumed. But in this case it is clear
what the rate law is, so there is no problem for tools to include it
when they write the SBML, and there is nothing to stop tools from
ignoring it when they read it. So I must admit that I am a bit puzzled
as to why it is such a big deal to make the math optional. What is the
harm in including it for completeness?
Yours,
--
Darren Wilkinson
email: darrenjwilkinson@btinternet.com
home www: http://www.darrenjwilkinson.btinternet.co.uk/
work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
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Posts: 5
Registered:
December 2005
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RE: SBML L2v2 specification vote #7: Making 'math'optional in KineticLaw
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23 Jan '06 16:05
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Dear all,
I thought the purpose of SBML was to develop a framework which could accept very different models.
SBML is absolutely excellent for representing simple and genome-scale metabolic models. Flux balance analysis is just ONE simple way to analyse these models. I simply do not understand why these models should not be permitted. Kinetics can be added afterwards. Good models are not developed by one person overnight. We add 'math' when we know the math!
Best, Thomas Grotkjær
________________________________
From: sbml-discuss-bounces@caltech.edu on behalf of Herbert Sauro
Sent: Tue 24/01/2006 00:35
To: SBML Discussion List
Subject: RE: [sbml-discuss] SBML L2v2 specification vote #7: Making 'math'optional in KineticLaw
There are a whole range of models which do not depend on rate laws,
probably the most ell know begin flux balance analysis, but others exist
to. However, SBML databasea such as biomodels.net do not consider these
to be valuable models and will not accept them into the database. So
perhaps rate law free models in SBML should not be permitted althohgh I
think otherwise.
Herbert Sauro
-----Original Message-----
From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
Sent: Thursday, January 19, 2006 1:28 PM
To: SBML Discussion List
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw
--- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > Any kind of local parameter is associated with a
> mathematical
> > > expression, be it for 'traditional ODE' modelling,
> stochastic
> > > modelling, or flux balance analysis.
> >
> > I'm not sure for logical modelling or petri net. Also, you
> can
>
> I am not sure either but not being sure is bad reason either way :).
Clearly you both need to read my book! ;-)
I'm certainly not aware of any modelling framework where a rate
parameter makes sense completely independently of any rate law.
There are frameworks where rates and rate laws are not used at all, but
then kinetic laws are not required, so we are all happy. There are also
frameworks where there is a _default_assumption_ about the nature of the
rate law (such as for stochastic petri nets and discrete stochastic
modelling more
generally) - namely that unless otherwise stated, irreversible
mass-action stochastic kinetics is assumed. But in this case it is clear
what the rate law is, so there is no problem for tools to include it
when they write the SBML, and there is nothing to stop tools from
ignoring it when they read it. So I must admit that I am a bit puzzled
as to why it is such a big deal to make the math optional. What is the
harm in including it for completeness?
Yours,
--
Darren Wilkinson
email: darrenjwilkinson@btinternet.com
home www: http://www.darrenjwilkinson.btinternet.co.uk/
work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
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Posts: 7
Registered:
February 2005
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 00:07
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As far as I understood it (correct me if I'm wrong here!) the issue is
not about whether rate law free models should be allowed in SBML or
not - they are allowed at present since the KineticLaw is not
compulsory. I also agree that these are valuable models and that they
should not be excluded from SBML.
However, the present discussion is around whether the 'math' should be
made optional if the KineticLaw is PRESENT. Here I agree with
Darren's sentiments (below) in that the math should indeed be
included explicitly. FBA models won't have KineticLaw but then there
also won't be a 'math' element in KineticLaw!
Johann Rohwer
On Tuesday, 24 January 2006 01:35, Herbert Sauro wrote:
> There are a whole range of models which do not depend on rate laws,
> probably the most ell know begin flux balance analysis, but others
> exist to. However, SBML databasea such as biomodels.net do not
> consider these to be valuable models and will not accept them into
> the database. So perhaps rate law free models in SBML should not be
> permitted althohgh I think otherwise.
>
> Herbert Sauro
>
> -----Original Message-----
> From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
> Sent: Thursday, January 19, 2006 1:28 PM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> --- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> > Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > > Any kind of local parameter is associated with a
> >
> > mathematical
> >
> > > > expression, be it for 'traditional ODE' modelling,
> >
> > stochastic
> >
> > > > modelling, or flux balance analysis.
> > >
> > > I'm not sure for logical modelling or petri net. Also, you
> >
> > can
> >
> > I am not sure either but not being sure is bad reason either way
> > :).
>
> Clearly you both need to read my book! ;-)
>
> I'm certainly not aware of any modelling framework where a rate
> parameter makes sense completely independently of any rate law.
> There are frameworks where rates and rate laws are not used at all,
> but then kinetic laws are not required, so we are all happy. There
> are also frameworks where there is a _default_assumption_ about the
> nature of the rate law (such as for stochastic petri nets and
> discrete stochastic modelling more
> generally) - namely that unless otherwise stated, irreversible
> mass-action stochastic kinetics is assumed. But in this case it is
> clear what the rate law is, so there is no problem for tools to
> include it when they write the SBML, and there is nothing to stop
> tools from ignoring it when they read it. So I must admit that I am
> a bit puzzled as to why it is such a big deal to make the math
> optional. What is the harm in including it for completeness?
>
> Yours,
>
>
> --
> Darren Wilkinson
> email: darrenjwilkinson@btinternet.com
> home www: http://www.darrenjwilkinson.btinternet.co.uk/
> work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
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Posts: 469
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October 2003
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RE: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 01:07
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On Mon, 23 Jan 2006, Herbert Sauro wrote:
> There are a whole range of models which do not depend on rate laws,
> probably the most ell know begin flux balance analysis, but others exist
> to. However, SBML databasea such as biomodels.net do not consider these
> to be valuable models and will not accept them into the database.
Herbert,
BioModels DB does not accept those models YET. And you know perfectly
that it is not because we don't find them valuable, but because of our
curation process. And FBA has explicitely been included in the scope
of MIRIAM.
--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223 494 521, Fax: +44(0)1223 494 468, Mob: +33(0)689218676
http://www.ebi.ac.uk/~lenov AIM screen name: nlenovere
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Posts: 123
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September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 05:59
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FBA also uses rate laws, these are of the type
v(i)=j(i) , for reaction i, and where where j(i) is a constant. Can be
written in MathML, no problems. In fact the whole FBA exercise is just a
parameter estimation problem where the j(i) have to be determined given a
set of linear constraints. No problem with this. What are the other
reactions without a rate law?
Pedro
On Monday 23 January 2006 18:35, Herbert Sauro wrote:
> There are a whole range of models which do not depend on rate laws,
> probably the most ell know begin flux balance analysis, but others exist
> to. However, SBML databasea such as biomodels.net do not consider these
> to be valuable models and will not accept them into the database. So
> perhaps rate law free models in SBML should not be permitted althohgh I
> think otherwise.
>
> Herbert Sauro
>
> -----Original Message-----
> From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
> Sent: Thursday, January 19, 2006 1:28 PM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> --- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> > Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > > Any kind of local parameter is associated with a
> >
> > mathematical
> >
> > > > expression, be it for 'traditional ODE' modelling,
> >
> > stochastic
> >
> > > > modelling, or flux balance analysis.
> > >
> > > I'm not sure for logical modelling or petri net. Also, you
> >
> > can
> >
> > I am not sure either but not being sure is bad reason either way :).
>
> Clearly you both need to read my book! ;-)
>
> I'm certainly not aware of any modelling framework where a rate
> parameter makes sense completely independently of any rate law.
> There are frameworks where rates and rate laws are not used at all, but
> then kinetic laws are not required, so we are all happy. There are also
> frameworks where there is a _default_assumption_ about the nature of the
> rate law (such as for stochastic petri nets and discrete stochastic
> modelling more
> generally) - namely that unless otherwise stated, irreversible
> mass-action stochastic kinetics is assumed. But in this case it is clear
> what the rate law is, so there is no problem for tools to include it
> when they write the SBML, and there is nothing to stop tools from
> ignoring it when they read it. So I must admit that I am a bit puzzled
> as to why it is such a big deal to make the math optional. What is the
> harm in including it for completeness?
>
> Yours,
>
>
> --
> Darren Wilkinson
> email: darrenjwilkinson@btinternet.com
> home www: http://www.darrenjwilkinson.btinternet.co.uk/
> work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 349
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RE: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 12:34
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I was thinking of things like elementary modes, conservation analysis,
investigating the global structure of networks (using clustering, power
law analysis etc) including modularity, and so on.
With respect to FBA one doesn't need an explict rate law (as you
mention), true one has boundary constraints, maybe technically one could
call them rate laws.
H
-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 6:00 AM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw
FBA also uses rate laws, these are of the type
v(i)=j(i) , for reaction i, and where where j(i) is a constant. Can be
written in MathML, no problems. In fact the whole FBA exercise is just a
parameter estimation problem where the j(i) have to be determined given
a set of linear constraints. No problem with this. What are the other
reactions without a rate law?
Pedro
On Monday 23 January 2006 18:35, Herbert Sauro wrote:
> There are a whole range of models which do not depend on rate laws,
> probably the most ell know begin flux balance analysis, but others
> exist to. However, SBML databasea such as biomodels.net do not
> consider these to be valuable models and will not accept them into the
> database. So perhaps rate law free models in SBML should not be
> permitted althohgh I think otherwise.
>
> Herbert Sauro
>
> -----Original Message-----
> From: Darren Wilkinson [mailto:darrenjwilkinson@btinternet.com]
> Sent: Thursday, January 19, 2006 1:28 PM
> To: SBML Discussion List
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> --- Stefan Hoops <shoops@vbi.vt.edu> wrote:
> > Nicolas Le Novere <lenov@ebi.ac.uk> wrote:
> > > On Tue, 17 Jan 2006, Stefan Hoops wrote:
> > > > Any kind of local parameter is associated with a
> >
> > mathematical
> >
> > > > expression, be it for 'traditional ODE' modelling,
> >
> > stochastic
> >
> > > > modelling, or flux balance analysis.
> > >
> > > I'm not sure for logical modelling or petri net. Also, you
> >
> > can
> >
> > I am not sure either but not being sure is bad reason either way :).
>
> Clearly you both need to read my book! ;-)
>
> I'm certainly not aware of any modelling framework where a rate
> parameter makes sense completely independently of any rate law.
> There are frameworks where rates and rate laws are not used at all,
> but then kinetic laws are not required, so we are all happy. There are
> also frameworks where there is a _default_assumption_ about the nature
> of the rate law (such as for stochastic petri nets and discrete
> stochastic modelling more
> generally) - namely that unless otherwise stated, irreversible
> mass-action stochastic kinetics is assumed. But in this case it is
> clear what the rate law is, so there is no problem for tools to
> include it when they write the SBML, and there is nothing to stop
> tools from ignoring it when they read it. So I must admit that I am a
> bit puzzled as to why it is such a big deal to make the math optional.
> What is the harm in including it for completeness?
>
> Yours,
>
>
> --
> Darren Wilkinson
> email: darrenjwilkinson@btinternet.com home www:
> http://www.darrenjwilkinson.btinternet.co.uk/
> work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 123
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 13:14
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On Tuesday 24 January 2006 15:34, Herbert Sauro wrote:
> I was thinking of things like elementary modes, conservation analysis,
> investigating the global structure of networks (using clustering, power
> law analysis etc) including modularity, and so on.
Sure, I agree that these are all extremely important things to do; but they
are already possible with SBML by simply representing the reaction network
without rate laws, as pointed out by several others here.
> With respect to FBA one doesn't need an explict rate law (as you
> mention), true one has boundary constraints, maybe technically one could
> call them rate laws.
They are rate laws because they are functions that describe the rate of
reaction. The rate laws themselves do not have constraints as long as they
have already been determined (their parameters).
The parameter estimation procedure is where the constraints operate, but
currently there is no way to specify parameter estimation because that is
not a model itself but rather a task operating on top of one, and SBML
currently only represents the models. (Though I believe there is a proposal
around that was discussed in Heidelberg last year, which would cover these
things) .
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 349
Registered:
September 2003
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RE: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 17:28
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These are good points but I don't think a model should be invalidated
because there is no kinetic law.
H
-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 1:14 PM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw
On Tuesday 24 January 2006 15:34, Herbert Sauro wrote:
> I was thinking of things like elementary modes, conservation analysis,
> investigating the global structure of networks (using clustering,
> power law analysis etc) including modularity, and so on.
Sure, I agree that these are all extremely important things to do; but
they are already possible with SBML by simply representing the reaction
network without rate laws, as pointed out by several others here.
> With respect to FBA one doesn't need an explict rate law (as you
> mention), true one has boundary constraints, maybe technically one
> could call them rate laws.
They are rate laws because they are functions that describe the rate of
reaction. The rate laws themselves do not have constraints as long as
they have already been determined (their parameters).
The parameter estimation procedure is where the constraints operate, but
currently there is no way to specify parameter estimation because that
is not a model itself but rather a task operating on top of one, and
SBML currently only represents the models. (Though I believe there is a
proposal around that was discussed in Heidelberg last year, which would
cover these
things) .
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 123
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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24 Jan '06 18:27
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But that is not the case. It is not invalidated, it is perfectly valid. The
current proposal (vote 7) is not about that, it is about having a kinetic
law without the math component. As several others have expressed, there is
no reason for that as it is already possible to have a reaction without a
rate law (which is what you were arguing). What does not make sense to me
is a rate law without the math (the expression of the rate law). No one is
arguing against reactions without rate laws...
P
On Tuesday 24 January 2006 20:28, Herbert Sauro wrote:
> These are good points but I don't think a model should be invalidated
> because there is no kinetic law.
>
> H
>
> -----Original Message-----
> From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
> Sent: Tuesday, January 24, 2006 1:14 PM
> To: sbml-discuss@caltech.edu
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> On Tuesday 24 January 2006 15:34, Herbert Sauro wrote:
> > I was thinking of things like elementary modes, conservation analysis,
> >
> > investigating the global structure of networks (using clustering,
> > power law analysis etc) including modularity, and so on.
>
> Sure, I agree that these are all extremely important things to do; but
> they are already possible with SBML by simply representing the reaction
> network without rate laws, as pointed out by several others here.
>
> > With respect to FBA one doesn't need an explict rate law (as you
> > mention), true one has boundary constraints, maybe technically one
> > could call them rate laws.
>
> They are rate laws because they are functions that describe the rate of
> reaction. The rate laws themselves do not have constraints as long as
> they have already been determined (their parameters).
>
> The parameter estimation procedure is where the constraints operate, but
> currently there is no way to specify parameter estimation because that
> is not a model itself but rather a task operating on top of one, and
> SBML currently only represents the models. (Though I believe there is a
> proposal around that was discussed in Heidelberg last year, which would
> cover these
> things) .
>
> --
> Pedro Mendes
> Research Associate Professor
> Virginia Bioinformatics Institute,
> Virginia Tech, Washington St.,
> Blacksburg, VA 24061-0477, USA
> http://mendes.vbi.vt.edu fax:+1-540-231-2606
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 349
Registered:
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RE: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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25 Jan '06 10:54
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Ok I see what you're saying, it makes sense. I have to admit I've not
been following the thread too closely which explains my confusion.
Herbert
-----Original Message-----
From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
Sent: Tuesday, January 24, 2006 6:27 PM
To: sbml-discuss@caltech.edu
Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
'math' optional in KineticLaw
But that is not the case. It is not invalidated, it is perfectly valid.
The current proposal (vote 7) is not about that, it is about having a
kinetic law without the math component. As several others have
expressed, there is no reason for that as it is already possible to have
a reaction without a rate law (which is what you were arguing). What
does not make sense to me is a rate law without the math (the expression
of the rate law). No one is arguing against reactions without rate
laws...
P
On Tuesday 24 January 2006 20:28, Herbert Sauro wrote:
> These are good points but I don't think a model should be invalidated
> because there is no kinetic law.
>
> H
>
> -----Original Message-----
> From: Pedro Mendes [mailto:mendes@vbi.vt.edu]
> Sent: Tuesday, January 24, 2006 1:14 PM
> To: sbml-discuss@caltech.edu
> Subject: Re: [sbml-discuss] SBML L2v2 specification vote #7: Making
> 'math' optional in KineticLaw
>
> On Tuesday 24 January 2006 15:34, Herbert Sauro wrote:
> > I was thinking of things like elementary modes, conservation
> > analysis,
> >
> > investigating the global structure of networks (using clustering,
> > power law analysis etc) including modularity, and so on.
>
> Sure, I agree that these are all extremely important things to do; but
> they are already possible with SBML by simply representing the
> reaction network without rate laws, as pointed out by several others
here.
>
> > With respect to FBA one doesn't need an explict rate law (as you
> > mention), true one has boundary constraints, maybe technically one
> > could call them rate laws.
>
> They are rate laws because they are functions that describe the rate
> of reaction. The rate laws themselves do not have constraints as long
> as they have already been determined (their parameters).
>
> The parameter estimation procedure is where the constraints operate,
> but currently there is no way to specify parameter estimation because
> that is not a model itself but rather a task operating on top of one,
> and SBML currently only represents the models. (Though I believe there
> is a proposal around that was discussed in Heidelberg last year, which
> would cover these
> things) .
>
> --
> Pedro Mendes
> Research Associate Professor
> Virginia Bioinformatics Institute,
> Virginia Tech, Washington St.,
> Blacksburg, VA 24061-0477, USA
> http://mendes.vbi.vt.edu fax:+1-540-231-2606
--
Pedro Mendes
Research Associate Professor
Virginia Bioinformatics Institute,
Virginia Tech, Washington St.,
Blacksburg, VA 24061-0477, USA
http://mendes.vbi.vt.edu fax:+1-540-231-2606
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Posts: 961
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Posts: 961
Registered:
October 2003
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Registered:
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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27 Jan '06 17:19
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shoops> Hello Mike, I still do not get why we need a
shoops> kinetic law without a math element. If I do not
shoops> know the mechanism I do not have a kinetic law. If
shoops> I know the mechanism (not only ODE) I have a
shoops> kinetic law and a mathematical expression. Our
shoops> problem is not the math element our problem is
shoops> that the math element only describes the right
shoops> side of an ODE in the current specification. In my
shoops> opinion this is the problem we need to attack. As
shoops> I have suggested earlier subclassing of the
shoops> kinetic law could be a solution. In addition we
shoops> can allow multiple kinetic laws for a reaction
shoops> each being from a different subclass.
Hi Stefan,
I only meant to propose the empty-math-interpretation as a
potential middle ground in the arguments on both sides. The
approach would have the advantage of answering the requests
made by some people for being able to have syntactically
valid SBML models that are incomplete. (But, these would
obviously not be considered fully characterized models.)
For example, the JigCell group (whose tool reads and writes
SBML as its "native" storage format) have noted that users
sometimes want to save a model even though it's not complete
and thus not fully characterized. If the tool is rigorously
checking syntax, writing out incomplete kinetic law elements
(for example) would be a no-no, leading to annoyance for the
user. Of course, there are other ways of coping with this,
but this is an example of the motivation for the idea above.
Other people recently noted that models are not developed
overnight, and pieces may be added over time. See, e.g.,
http://www.sbml.org/forums/index.php?t=tree&goto=2972&rid=0
Let's turn to the idea of subclassing for a moment. The
difficulty with subclasses that I see is they have to be
defined in the specification as permissible syntactic data
structures, and we don't (and probably can't) have a settled
list of these types. So how would we write the SBML
specification for these subclasses? Maybe I'm missing
something obvious. (Wouldn't be the first time.)
But along the lines of your suggestion, I'd like to throw
out the following idea. What if Reaction were defined to
have not one KineticLaw, but a list of KineticLaws? A model
would then look like this:
<reaction id="J1">
<listOfReactants>
...
</listOfReactants>
<listOfProducts>
...
</listOfProducts>
<listOfKineticLaws>
<kineticLaw sboTerm="..."> <!-- 1st one -->
<math xmlns="...">
...
</math>
<listOfParameters>
...
</listOfParameters>
</kineticLaw>
<kineticLaw sboTerm="..."> <!-- another one -->
<math xmlns="...">
...
</math>
<listOfParameters>
...
</listOfParameters>
</kineticLaw>
</listOfKineticLaws>
</reaction>
The specification would state that if a tool cannot deal
with alternative formulations, it can take the first law in
the list. Most models would have only one kinetic law
anyway.
Some tools would be more advanced and allow a user to
explicitly define alternative kinetic laws for different
simulation frameworks. For example, one might be for ODEs,
while another (or maybe even more than one) kinetic law in
the list might be for discrete stochastic simulation, and so
on.
The main difficulty I've been having with this idea is
coming up with a scheme for establishing correspondence
between the kinetic laws defined in different reactions.
Basically, the problem is, if you have two reactions R1 and
R2, and each has multiple kinetic laws, how do you know
which kinetic laws to use if you're doing a simulation?
In the example above, I show the use of sboTerm attributes
on the kineticLaws, the idea being that the attribute would
point to controlled vocabulary terms standing for
"continuous deterministic simulation framework", "petri net
framework", etc. But that's not the only way it could go.
Here are the alternatives that come to my mind:
a) Use sboTerm tags as above.
b) Do it by position. All the first laws in every reaction
woudl implicitly be grouped together, all the second laws
would be grouped together, etc. Problems with this idea
include: what if two reactions don't have the same number
of kinetic laws? What if one reaction is supposed to
translate to multiple kinetic laws in a certain
framework? Basically, this approach seems fragile.
c) Use a new attribute giving a sequence number for each
kineticLaw -- something that says essentially law=1,
law=2, etc., and the specification would stipulate that
all laws labeled #1 would belong together, all laws
labeled #2 would belong together, etc. This seems more
robust than alternative (b), but still doesn't address
the possibility of a reaction requiring multiple rate
laws in some given framework.
d) Have some sort of type attribute on the kineticLaw
elements, like type="something". I feel this is no
different than using sboTerms, and is actually worse,
because it would require us to agree and prescribe a
separate list of terms. There are obvious problems with
maintenance, evolution, and error correction.
Anyway, this is just an idea. I'm curious to hear what
people thing. It might be stupid, but I'm prepared to take
the flames ;-).
MH
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Posts: 96
Registered:
September 2003
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Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
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30 Jan '06 05:18
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Hello Mike,
Your suggestion goes exactly along the lines I am thinking. We have
different kinetic laws for different interpretations of the model. The
sboTerm or sublcassing could be used to identify the intended
interpretation the author had in mind. I am still not sure what the best
approach is. Subclassing gives us the freedom to modify the the
kineticlaw element for each interpretation (adding attributes and
elements), which is somehow richer than sboTerms. However, the sboTerm
is in my opinion easier to extend. May be a combination of both is the
best.
Regarding the storage of incomplete models in SBML we have the same
issues within COPASI. But we came to the conclusion that SBML is
perfectly able to handle incomplete models. Reactions are not required
to have kinetic laws therefore a not fully defined kinetic model can be
stored in SBML. This model however may allready complete in the view of
its connectivity since substrates, products, and modifier can be
specified. Adding a partial kinetic law does not gain anything since the
parameters are only meaningful with the math in mind. And therefore the
math element can be written.
Thanks,
Stefan
On Fri, 27 Jan 2006 17:19:49
-0800 Michael Hucka <mhucka@caltech.edu> wrote:
> shoops> Hello Mike, I still do not get why we need a
> shoops> kinetic law without a math element. If I do not
> shoops> know the mechanism I do not have a kinetic law. If
> shoops> I know the mechanism (not only ODE) I have a
> shoops> kinetic law and a mathematical expression. Our
> shoops> problem is not the math element our problem is
> shoops> that the math element only describes the right
> shoops> side of an ODE in the current specification. In my
> shoops> opinion this is the problem we need to attack. As
> shoops> I have suggested earlier subclassing of the
> shoops> kinetic law could be a solution. In addition we
> shoops> can allow multiple kinetic laws for a reaction
> shoops> each being from a different subclass.
>
> Hi Stefan,
>
> I only meant to propose the empty-math-interpretation as a
> potential middle ground in the arguments on both sides. The
> approach would have the advantage of answering the requests
> made by some people for being able to have syntactically
> valid SBML models that are incomplete. (But, these would
> obviously not be considered fully characterized models.)
>
> For example, the JigCell group (whose tool reads and writes
> SBML as its "native" storage format) have noted that users
> sometimes want to save a model even though it's not complete
> and thus not fully characterized. If the tool is rigorously
> checking syntax, writing out incomplete kinetic law elements
> (for example) would be a no-no, leading to annoyance for the
> user. Of course, there are other ways of coping with this,
> but this is an example of the motivation for the idea above.
>
> Other people recently noted that models are not developed
> overnight, and pieces may be added over time. See, e.g.,
> http://www.sbml.org/forums/index.php?t=tree&goto=2972&rid=0
>
> Let's turn to the idea of subclassing for a moment. The
> difficulty with subclasses that I see is they have to be
> defined in the specification as permissible syntactic data
> structures, and we don't (and probably can't) have a settled
> list of these types. So how would we write the SBML
> specification for these subclasses? Maybe I'm missing
> something obvious. (Wouldn't be the first time.)
>
> But along the lines of your suggestion, I'd like to throw
> out the following idea. What if Reaction were defined to
> have not one KineticLaw, but a list of KineticLaws? A model
> would then look like this:
>
> <reaction id="J1">
> <listOfReactants>
> ...
> </listOfReactants>
> <listOfProducts>
> ...
> </listOfProducts>
> <listOfKineticLaws>
> <kineticLaw sboTerm="..."> <!-- 1st one -->
> <math xmlns="...">
> ...
> </math>
> <listOfParameters>
> ...
> </listOfParameters>
> </kineticLaw>
> <kineticLaw sboTerm="..."> <!-- another one -->
> <math xmlns="...">
> ...
> </math>
> <listOfParameters>
> ...
> </listOfParameters>
> </kineticLaw>
> </listOfKineticLaws>
> </reaction>
>
> The specification would state that if a tool cannot deal
> with alternative formulations, it can take the first law in
> the list. Most models would have only one kinetic law
> anyway.
>
> Some tools would be more advanced and allow a user to
> explicitly define alternative kinetic laws for different
> simulation frameworks. For example, one might be for ODEs,
> while another (or maybe even more than one) kinetic law in
> the list might be for discrete stochastic simulation, and so
> on.
>
> The main difficulty I've been having with this idea is
> coming up with a scheme for establishing correspondence
> between the kinetic laws defined in different reactions.
> Basically, the problem is, if you have two reactions R1 and
> R2, and each has multiple kinetic laws, how do you know
> which kinetic laws to use if you're doing a simulation?
>
> In the example above, I show the use of sboTerm attributes
> on the kineticLaws, the idea being that the attribute would
> point to controlled vocabulary terms standing for
> "continuous deterministic simulation framework", "petri net
> framework", etc. But that's not the only way it could go.
> Here are the alternatives that come to my mind:
>
> a) Use sboTerm tags as above.
>
> b) Do it by position. All the first laws in every reaction
> woudl implicitly be grouped together, all the second laws
> would be grouped together, etc. Problems with this idea
> include: what if two reactions don't have the same number
> of kinetic laws? What if one reaction is supposed to
> translate to multiple kinetic laws in a certain
> framework? Basically, this approach seems fragile.
>
> c) Use a new attribute giving a sequence number for each
> kineticLaw -- something that says essentially law=1,
> law=2, etc., and the specification would stipulate that
> all laws labeled #1 would belong together, all laws
> labeled #2 would belong together, etc. This seems more
> robust than alternative (b), but still doesn't address
> the possibility of a reaction requiring multiple rate
> laws in some given framework.
>
> d) Have some sort of type attribute on the kineticLaw
> elements, like type="something". I feel this is no
> different than using sboTerms, and is actually worse,
> because it would require us to agree and prescribe a
> separate list of terms. There are obvious problems with
> maintenance, evolution, and error correction.
>
> Anyway, this is just an idea. I'm curious to hear what
> people thing. It might be stupid, but I'm prepared to take
> the flames ;-).
>
> MH
>
>
>
>
--
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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Posts: 961
Registered:
October 2003
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Posts: 961
Registered:
October 2003
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