Re: [SOSlib-devel] Request for help with a multicompartment problem

[Nicolas Le N. <le...@eb...>]

On Mon, 11 Sep 2006, Andrew Finney wrote:

> Assuming the issue is just how to create an encoding in SBML for
> multicomparment models
> and not how to map from SBML to ODEs...
>
> I'd just like to point out one obvious point...
>
> an equation like
>
> d[C]/dt = k * [A] * [B]
>
> describes a phenomena that only really works in a single compartment.
> i.e. when two species are in the same compartment and therefore can freely
> react with each
> other the rate of reaction is proportional to the concentrations of the
> species.
>
> if A B and C are not in the same compartment the equation doesn't make any
> physical sense to describe the interactions
>
> in that case any chemical equation A + B -> C
> has be decomposed into its constituent transport and conversation components
> before you can move forward,

But that is the point. Developing a model implies a balance of
abstraction Vs. biological exactitude. I recently submitted a paper
describing a model with 159 reactions. Two-third of them involve
various states of just one molecule. On the contrary, the remaining
reactions are mainly phenomenological descriptions of all the others
participants. And that's fine. Because we don't care much about
them. We just want them to behave as we think they are in the cell.

If that suits me, I can perfectly model degradation of mRNA using a
RNAse in the cytosol and the mRNA in the nucleus, without modeling the
transport of RNA. No referee will reject my model, except if it deals
specifically with RNA degration (funny enough regarding the model
cited above, we braced ourselves against the referee's criticisms on
the way we modeled second-knives and prepared alternative version of
the model. But none of the three referees - who did a very thorough
job and required a huge number of modifications - even mentioned the
issus).

IMHO, it is not our job, as SBML developers, to decide how a modeller
should formulate the model.


-- 
Nicolas LE NOVERE,  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, AIM: nlenovere,  MSN: nle...@ho...