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Uh oh.

Wow, I didn't see *that* one coming.

And no way around it, either, huh?

John Wagner, PhD
Functional Genomics & Systems Biology
IBM T.J. Watson Research Center
P.O.Box 218 Office : (914) 945-3079
Yorktown Heights, NY 10598 Fax : (914) 945-4104
wagnerjo@us.ibm.com
http://www.research.ibm.com/FunGen/index.html




Nicolas Le Novere <lenov@ebi.ac.uk>
Sent by: sbml-discuss-bounces@caltech.edu
04/29/2005 05:05 AM
Please respond to SBML Discussion List

To: sbml-discuss@caltech.edu
cc:
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