Forums

Hugh and yourself are right of course. But I'm not asking how, as a
modeler, I should avoid that. The answer is just "don't be dumb". My
problem is as a recipient of the model. I receive the model AS IT
IS. What can I do with it?

For the immediat purposes of BioModels and SBMLeditor, such as
printing the ratelaw, we will just overide everything by the local
ids. But I'm convinced it is a problem that we should address, and the
sooner the better.

For Level2 version2 I propose to follow what is implied by you
suggestion and PUT ALL THE ID IN THE SAME NAMESPACE, using only the
"name" when we want to use the same parameter with different local
values. I know why we create the local namespaces in the first place,
but retrospectively that was not a good idea.

Could SBML users provide examples where that would be a problem
unfixable by the use of prefixes?


On Fri, 29 Apr 2005, Stefan Hoops wrote:

> Hello Nicolas,
>
> I think in level 2 this problem can easily solved by using the name and
> id fields. Please see below:
>
> <listOfCompartments>
> <compartment id="c_1" name="cyt" size="5e-15"/>
> <compartment id="c_2" name="nuc" size="e-15"/>
> </listOfCompartments>
> <listOfSpecies>
> <species id="A" compartment="c_1" initialConcentration="0.5"/>
> <species id="B" compartment="c_2" initialConcentration="0"/>
> </listOfSpecies><listOfReactions>
> <reaction id="transport">
> <listOfReactants>
> <reactant speciesReference="A" />
> </listOfReactants>
> <listOfProducts>
> <product speciesReference="B">
> </listOfProducts>
> <kineticLaw>
> <math>
> <apply>
> <minus/>
> <apply>
> <times/>
> <ci>nuc</ci>
> <ci>A</ci>
> <ci>c_1</ci>
> </apply>
> <apply>
> <times/>
> <ci>cyt</ci>
> <ci>B</ci>
> <ci>c_2</ci>
> </apply>
> </apply>
> </math>
> <listOfParameters>
> <parameter id="cyt" value="0.1" />
> <parameter id="nuc" value="0.01" />
> </listOfParameters>
> </kineticLaw>
> </reaction>
> </listOfReactions>
>
> Thanks,
> Stefan
>
>

--
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 AIM screen name: nlenovere