convertToSBML

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convertToSBML[network, ic, rates, id, name, compartment] converts an xlr8r model into SBML Level 2 Version 1

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Requires xlr8r 0.25, MathSBML 2.5.25, xlr8r2SBML.m

network is any xlr8r model that is compatable with interpret.

ic is any list of xlr8r initial conditions such as {x₁->a₁, x₂->a₂,...}.

rates is any list of replacement rules that will be converted to SBML parameter values, as in {a->27, b->3, ...}

id is the desired SBML model id.

name is the desired SBML model name.

compartment is the desired SBML compartment id.

The output of is an XML string.

Example

        <<xlr8r.m;
        <<mathsbml.m;
        <<xlr8r2SBML.m;
        ...
        (* define the model *)
        m={{A+En->X, k1},{X->A+En, k2}, {X->B+En, k3}};
        r={k1->0.01, k2->0.05, k3->1};
        ic={A->1, En->1, B->0};
        ...
        (* do stuff in xlr8r with the model *)
        ...
        interpret[m]
        {{A'[t]==-k1 A[t] En[t] + k2 X[t], 
             B'[t]==k3 X[t],
             En'[t]= ...}
            {A, B, En, X}
        ...
        (* generate SBML for the model *)
        sbml=convertToSBML[m, ic, rates, "enzmod", 
           "Simple Enzymatic Reaction", "cell"];
        ...
        (* Save the sbml to an xml file *)       
        Export["myfile.xml", sbml];

Implementation Notes

• Models are converted to SBML Level 2 Version 1.

See also

• SBML2xlr8r