Forums

OK, I re-explain:

We have:

a global id "cyt" representing the cytoplasm: 5e-15 litre
a global id "nuc" representing the nucleus: e-15 litre
a local id "cyt" representing the export to the cytoplam: 0.1 s-1
a local id "nuc" representing the export to the nucleus: 0.01 s-1

Because the species are expressed in concentration, I have to multiply
their symbol by the volume of their compartment to model a transport
of substance:

Transport of A from the cytoplasm to the nucleus:

0.01 x A x e-15 => nuc x A x cyt

Transport of B from the nucleus to the cytoplasm:

0.1 x B x e-15 => cyt x B x nuc

...

On Fri, 29 Apr 2005, Colin Gillespie wrote:

> >So our equation
> >
> >dB/dt = 0.01 x A x 5e-15 - 0.1 x B x e-15
> Did you mean
> dB/dt = e-15 x A x 5e-15 - 5e-15 x B x e-15?
>
> >is transformed into
> >
> >dB/dt = 0.01 x A x 0.1 - 0.1 x B x 0.01
>
> Yes, that's what I thought
>
>
> >On Fri, 29 Apr 2005, Colin Gillespie wrote:
> >
> >> I always thought that the local parameters took preference over
> >> everything else.
> >>
> >> So in this case the values are {cyt, nuc} = {0.1, 0.01}
> >>
> >> Colin
> >> >-----Original Message-----
> >> >From: sbml-discuss-bounces@caltech.edu
> >> >[mailto:sbml-discuss-bounces@caltech.edu] On Behalf Of Nicolas
> >> >Le Novere
> >> >Sent: 29 April 2005 10:06
> >> >To: sbml-discuss@caltech.edu
> >> >Subject: [sbml-discuss] parameters and namespaces
> >> >
> >> >
> >> >In the following fake (dumb) code, how can I interpret the
> >> >ratelaw, i.e. what are the values of "cyt" and "nuc"?
> >> >
> >> ><listOfCompartments>
> >> > <compartment id="cyt" size="5e-15"/>
> >> > <compartment id="nuc" size="e-15"/>
> >> ></listOfCompartments>
> >> ><listOfSpecies>
> >> > <species id="A" compartment="cyt" initialConcentration="0.5" />
> >> > <species id="B" compartment="nuc" 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>cyt</ci>
> >> > </apply>
> >> > <apply>
> >> > <times/>
> >> > <ci>cyt</ci>
> >> > <ci>B</ci>
> >> > <ci>nuc</ci>
> >> > </apply>
> >> > </apply>
> >> > </math>
> >> > <listOfParameters>
> >> > <parameter id="cyt" value="0.1" />
> >> > <parameter id="nuc" value="0.01" />
> >> > </listOfParameters>
> >> > </kineticLaw>
> >> > </reaction>
> >> ></listOfReactions>
> >> >
> >> >--
> >> >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
> >> >
> >> >
> >> >
> >>
> >>
> >
> >--
> >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
> >
> >
> >
>
>

--
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