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Hi Andrew,


I just wanted to recap part of my previous posting for you:

-------------
((Namespace))

I strongly support having local namespaces. We will find this
useful if SBML decides to use the reaction mechanism above
or whatever similar some time. A reaction mechanism could
have 'ports' that connects internal representations of species
and parameters with those given by a reaction instance.

This might be a different thing, but we sometimes find it annoying
SBML's not having a separate namespace for each compartment.
Compartments are hierarchical anyway, so we may find it cleaner
to use some kind of path representations, such as
Cell0.Cytosol.Mitochondrion0.Matrix.ATP or,
in E-Cell, /CELL0/CYTOSOL/MITOCHONDRION0/MATRIX:ATP.
When exporting from E-Cell to SBML level 1/2, currently we cannot
just use 'ATP', but are forced to mangle this name like
'CELL0__CYTOSOL__MITOCHONDRION0__MATRIX__ATP'.
-------------


If SBML intends to support compartmental modeling, frankly,
we are puzzled why the spec is like this. Actually I remember
I proposed a kind of structural namespace like I described above
in the early days of SBML Forum when we were trying to reach
level 1 version 1. It may have been my failure not having been able
to clearly present the idea, or it looked too E-Cell-centric
to the rest of SBML Forum at that time...



-Kouichi


> Nicolas
>
>> If the namespaces of
>> parameters and compartments are separated in the modeling environment,
>> which is the case in *every* software I'm aware of, the
>> problem occur not
>> in the model, but in the SBML encoding of the model.
>
> Please give examples of these software packages.
>
> yours
> Andrew Finney
>
>> -----Original Message-----
>> From: sbml-discuss-bounces@caltech.edu
>> [mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of
>> Nicolas Le Nov$BoS(Be
>> Sent: 30 April 2005 15:26
>> To: SBML Discussion List
>> Subject: Re: [sbml-discuss] parameters and namespaces
>>
>> > Also note that the units of
>> > 0.01 and 0.1 are unspecified.
>>
>> There are default units. If all the id are correctly mapped.
>> There is no
>> ambiguity on the unit, since the result should always be
>> substance/time.
>>
>>
>> > d[A] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
>> > ---- = - ---------------------------------------
>> > dt volume_of_compartment_cyt
>> >
>> > What is 'volume_of_compartment_cyt'? It is given in the
>> > definition of compartment 'cyt' as 5e-15. Hence,
>> >
>> > d[A] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
>> > ---- = - ---------------------------------------
>> > dt 5e-15
>> >
>> > Similarly for the rate of change of the concentration of B:
>> >
>> > d[B] (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
>> > ---- = ---------------------------------------
>> > dt volume_of_compartment_nuc
>> >
>> >
>> > (0.01 * [A] * 0.1) - (0.1 * [B] * 0.01)
>> > ---------------------------------------
>> > 1e-15
>>
>> We agree on that. But this is not the correct result. The
>> results intended
>> by the author was:
>>
>> > d[A] (0.01 * [A] * 5e-15) - (0.1 * [B] * 1e-15)
>> > ---- = - ---------------------------------------
>> > dt 5e-15
>> >
>> > d[B] (0.01 * [A] * 5e-15) - (0.1 * [B] * 1e-15)
>> > ---- = ---------------------------------------
>> > dt 1e-15
>> >
>>
>> > The given example in my mind is
>> > a problem that falls squarely in the lap of the model
>> > author: they created a bad model.
>>
>> Yes if we consider here the model "author" as the sum of the model
>> creators and the developers of the SBML export. If the namespaces of
>> parameters and compartments are separated in the modeling environment,
>> which is the case in *every* software I'm aware of, the
>> problem occur not
>> in the model, but in the SBML encoding of the model.
>>
>>
>> --
>> Nicolas LE NOV$B%M(BRE, 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
>>
>>
>>
>
>