Re: SBML L2v2 specification vote #7: Making 'math' optional in KineticLaw
24 Jan '06 00:07
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!
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:email@example.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 <firstname.lastname@example.org> wrote:
> > Nicolas Le Novere <email@example.com> 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?
> Darren Wilkinson
> email: firstname.lastname@example.org
> home www: http://www.darrenjwilkinson.btinternet.co.uk/
> work www: http://www.staff.ncl.ac.uk/d.j.wilkinson/