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Schaff,Jim wrote:

> In a single compartment model, the presence of multiple sbml:species is
> an explicit statement by the modeler that each sbml:species is
> structurally and functionally distinct. For multi-compartmental models,
> especially those that include transport/trafficking, the SBML Level 2
> element sbml:speciesType allowed the modeler to unambiguously indicate
> which sbml:species corresponded to the "same" molecular entity. For
> example, there is no separate "transport" mechanism defined within SBML,
> and without knowing the relationships between reactants and products,
> the intent of the modeler is lost.

Not at all. A reaction X -> Y where X is one compartment and Y is in
another is a transport. That is the intent of the modeler. If the modeler
intended to imply something else, he should describe it.

> Oliver brings up an interesting and controversial question, why do we
> have sbml:compartments?
>
> Solely in terms of the mathematics of simulation, the sbml:species are
> distinct molecular pools (molecular entities located in a compartment)
> which are the state variables of the system. These molecular pools need
> an initial condition (stored with the pool) and a size for calculating
> concentrations (currently stored in an external object -
> sbml:compartment).

No. That would be true if the unit of the species were all the same, and
the same than the unit of the kineticLaw multiplied by the stoichiometry.

> We have sbml:compartments because they are important to the biological
> semantics of the model. Otherwise, if sbml:compartment was used only to
> provide a container for a shared "size" parameter, we could use a model
> parameter instead.

No. Because compartment have a dimension, and this dimension affects the
behaviour of the model.

> Level 3 extensions
> ==================

> It remains unclear how easy it
> will be for most of the 170 SBML tools to support ANY of the Level 3
> extensions unless they are seamlessly integrated within libSBML. Given
> that, support for molecular entities will be very sparse if they are not
> in the Core.

Excuse-me but then, why those tools should use L3 at all? Why not sticking
to L2.

--
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nlenovere@hotmail.com(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/


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