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Hello Nicolas, All,

On Tue, Sep 8, 2009 at 6:41 PM, Nicolas Le novère<lenov@ebi.ac.uk> wrote:
>> Optionally, use a parameter.
>
> Not that simple: you need to define the dimension of a compartment.

I agree, compartments make life easier. But you could model without
them, if you had to.

> Because the string "phosphorylated_mapk" is just a set of bits that have no
> particular meaning. For instance, you cannot relate it to
> "phosphorylated_cyclin" or "phosphorylated_mapkk".

I agree that having an entity alone does not make you know what
entity it is. But just knowing that two species are the same entity is
worth a lot.

>>   No you can not do it with names, because there is no standard for
>> it.
>
> And? There is no standard for SpeciesType either.

If you make it part of L3 Core, then it would be a standard we could
rely upon. There may be alternatives, but you would have to propose
them first and get them accepted.

>>   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.
>
> Ah ... OK. I thought we were talking about SBML Level 3. Sorry for my
> misunderstanding.

Sorry if I wasn't clear. My point is, if it can be removed easily,
it can not be essential. It is a hypothetical change of L2 or L3.

> I am very willing to talk about redesigning SBML for
> Level 4. I actually have pretty precise ideas on how to do it for cleanly
> separating model structure, biological semantics and model display. I
> believe we will converge on this actually.

Sounds interesting! I would like to hear that. Feel free to open a
new thread about this.

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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