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A compartmentType is a class of compartments. Compartments can refer
to compartmentType 'id', and this 'id' can be used in generalized
reactions.


<listOfCompartmentType>
<compartmentType id="mito" />
</listOfCompartmentType>
<listOfSpeciesType>
<speciesType id="ATP" />
<speciesType id="ADP" />
</listOfSpeciesType>
<listOfCompartment>
<compartment id="cytosol" />
<compartment id="mito1" compartmentType="mito" />
<compartment id="mito2" compartmentType="mito" />
</listOfCompartment>
<listOfSpecies>
<species id="ATP_cytosol" speciesType="ATP" compartment="cytosol" />
<species id="ADP_cytosol" speciesType="ADP" compartment="cytosol" />
<species id="ATP_mito" speciesType="ATP" compartment="mito" />
<species id="ADP_mito" speciesType="ADP" compartment="mito" />
</listOfSpecies>
<listOfReactions>
<reaction id="ATPase">
<listOfReactants>
<speciesReference species="ATP" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP" >
</listOfProducts>
</reaction>
</listOfReactions>

This creates three reactions. The first expansion is based on the
speciesType (I use SBML to explain, but of course, intermediate SBML
files should not be used.):

<reaction id="ATPase_cytosol">
<listOfReactants>
<speciesReference species="ATP_cytosol" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP_cytosol" >
</listOfProducts>
</reaction>

<reaction id="ATPase_mito">
<listOfReactants>
<speciesReference species="ATP_mito" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP_mito" >
</listOfProducts>
</reaction>

Since ATP_mito and ADP_mito point to a generalized compartment, a
second expansion is performed:

<reaction id="ATPase_cytosol">
<listOfReactants>
<speciesReference species="ATP_cytosol" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP_cytosol" >
</listOfProducts>
</reaction>

<reaction id="ATPase_mito1">
<listOfReactants>
<speciesReference species="ATP_mito1" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP_mito1" >
</listOfProducts>
</reaction>

<reaction id="ATPase_mito2">
<listOfReactants>
<speciesReference species="ATP_mito2" >
</listOfReactants>
<listOfProducts>
<speciesReference species="ADP_mito2" >
</listOfProducts>
</reaction>

Note that the species ATP_mito1 and ATP_mito2 have obligatory the same
initialAmount or initialConcentration.


--
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