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.