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Nicolas

you wrote:

> > Any change to SBML to deal with this issue would have to be
> introduced
> > into SBML Level 2 Version 2 (L2V2).
>
> I am not sure to understand that. Why does it have to be introduced in
> L2V2 rather than postponed?
>

You are right we can postpone this decision.
I just meant to say that L2V2 is the earliest we can introduce this.
This kind of change is beyond the scope of an errata.

> > Possible Options for change
> > ===========================
> >
...
> d) add listOfStateVariables
>
> Those state variables can be any observables, already
> declared as species
> OR parameter OR compartment (the volume of a compartment can
> be a state
> variable!)

I don't understand the motivation for this:
species, parameter and compartment can all be declared as variables
by setting constant = false (which is the default for species).

What's the problem you are trying to solve?
What is the form of a state variable structure?

yours
Andrew Finney

> -----Original Message-----
> From: sbml-discuss-bounces@caltech.edu
> [mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of
> Nicolas Le Novère
> Sent: 19 February 2006 19:05
> To: SBML Discussion List
> Subject: RE: [sbml-discuss] Suggestion for new section in SBML
>
>
> > Any change to SBML to deal with this issue would have to be
> introduced
> > into SBML Level 2 Version 2 (L2V2).
>
> I am not sure to understand that. Why does it have to be introduced in
> L2V2 rather than postponed?
>
> > I strongly believe we should maintain as much backwards capability
> > between SBML L2V2 and Level 2 Version 1 (L2V1) as possible
> i.e. so that
> > a L2V1 model is a valid L2V2 model (with an appropriate
> change to the
> > document preamble).
>
> Yes. I entirely agree with that. L2V2 is not a new level.
>
> > Possible Options for change
> > ===========================
> >
> > a) do nothing
>
> Yes for now.
>
> > b) add 'listOfVariables' to 'model'
> > --------------------------------
>
> > c) add 'listOfSymbols' to 'model'
> > ------------------------------
>
> d) add listOfStateVariables
>
> Those state variables can be any observables, already
> declared as species
> OR parameter OR compartment (the volume of a compartment can
> be a state
> variable!)
>
> --
> 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
>
>