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Hello Nicolas, All,

On Tue, Sep 8, 2009 at 12:12 PM, Nicolas Le novère<lenov@ebi.ac.uk> wrote:
> Oliver Ruebenacker wrote:
>>   If size was the only issue, you could have that more easily and more
>> flexibly by adding a size attribute to the species. Compartments would
>> be an unjustified overkill.
>
> No, no, no. We are talking about quantitative models here. 1) you need a
> symbol for representing the compartment in equations and 2) you need to
> enforce consistency so that the compartment of all the relevant species is
> maintained at the same value.

Just plug in the same value everywhere where the same value is
needed. That's easy. Optionally, use a parameter.

> SBML is not BioPAX and vice-versa (otherwise we would not need two
> languages). In BioPAX, one is interested in the conceptual relationships
> between entities. This is why compartment was, in L2, an attribute of a
> physicalEntityParticipant. In SBML, the purpose is to encode models with
> rules describing the evolution of the model.

Rest assured that I know the difference between SBML and BioPAX. I
published papers on this precise issue.

>>   Of course it has to do with the current debate. You brought up
>> annotations as an argument against species types
>
> No, I did not. I say that if you need to describe precisely biological
> knowledge that does not affect the interpretation of the model, you must
> use annotation.

That's the same.

> The debate is (or should be) on how to group species in a larger set that
> one can identify. The proposal of Robert was to use another label such
> "phosphorylated_mapk", that would cover all the phosphorylated MAPK,
> whether in the cytoplasm or the nucleus. This is different to encode in a
> computationally usable framework the fact that this "species type"
> represent the set of all proteins in the cell that have the same nucleotide
> sequence and are phosphorylated.

How is it different?

>>   All we want is being able to say that two species within the same
>> model are the same entity. You can do that perfectly with species
>> types, even if they are called jack and jill.
>
> And you already can with the name. And you will be able with the groups.

No you can not do it with names, because there is no standard for
it. If you want to propose to add such a standard to L3 Core, go
ahead. We want something in Core, and we want it existing. Groups are
neither.

>>   We need to have entities in the SBML Core, not some package, because
>> entities are essential to the semantics of SBML. As essential as
>> compartments.
>
> No, it is not. If you load an SBML file in a simulator, any simulator, with
> or without specieTypes, and click run, you get exactly the same curves. If
> you suppress the compartments, you cannot reconstruct the ODEs.

It's trivial to redesign SBML to make compartments obsolete.
Compartment size is just a little number that can be easily moved
somewhere else. You can justify compartments on philosophical grounds,
or argue with traditions, but you can not defend them based on
mathematical necessity.

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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