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>> The advantage is that one can modify the volume of the signalling
>> compartment without touching the metabolic one (for instance, to embed
>> the post-synaptic signalling compartment into a dendritic spine.)
>
> In your example, you considered independently changing the volume of the
> "post-synaptic signaling" compartment to embed it into a dendritic spine
> (which is a geometrically distinct physical location).

No it is not. I badly selected my words as usual. In my example, the
dendritic spine *contains* the post-synaptic density. It is not a
surrounding relationship like we would have with the SBML attribute
"outside". The metabolic reactions would take place in the whole spine,
while some signalling reactions would take place in only a subvolume (e.g.
regulation of CaMKII phosphorylation). In order to that, one can use two
SBML compartments and distribute the species adequately. See the EGFR
model of Schoeberl (2002) Nat Biotech, for another example.

But all that has nothing to do with compartmentTypes. It is about the
usage of SBML compartments. Therefore I suggest we stop here :-)

--
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