SBML2xlr8r

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SBML2xlr8r[filename, options] reads an SBML file into an xlr8r model.

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Requires xlr8r 0.25, MathSBML 2.5.25, and Mathematica 5.1

filename is the name of the SBML file.

options are any valid options for MathSBML`SBMLRead.

The return value has the form

	{xCelleratorNetwork→{reaction1, reaction2...},
	 xCelleratorIC→{x1→val1, x2→val2,...}, 
	 xCelleratorRates→{r1→v1, r2→v2,...}}

where reaction₁,... are standard cellerator arrow forms; x_i are cellerator variables defined in the reactions; val_i is the initial value for cellerator variable x_i; r_i→v_i is a Mathematica rule that should be applied to the system.

Example

	<<xlr8r.m
	<<mathsbml.m
	<<SBML2xlr8r.m
	...
	m=SML2xlr8r[filename];
	net=xCelleratorNetwork/.m;
	ic=xCelleratorRates/.m;
	r=xCelleratorRates/.m;
	i=interpret[net]/.r;
	sim=run[i, initialConditions→ic, rates→r];
	runPlot[sim]

Implementation Notes

• Events in the SBML Model are ignored. Event compatibility will be added in the future.
• Functions in the SBML Model are ignored. Function compatibility will be added in the future.
• Algebraic Rules in the SBML Model rules are ignored. Algebraic rule compatibility will be added in the future.
• Reactions are converted to xCellerator mass-action reactions or xCellerator user reactions.
• In general the model is immediately xCellerator compatible:

  	m=SBML2xlr8r[filename];
  	n=interpret[ xCelleratorNetwork/.m ];		
  	r=run[n//. (xCelleratorRates/.m), 
  	      initialConditions→(xCelleratorIC/.m)];
  

  However, if algebraic rules, events, or functions are defined in the model the run command will either cause an error (because of undefined variables or missing information) or will produce results that the modeler did not intend.
• Only SBML Level 2 is supported. Level 1 models should first be converted to level 2 using the online-converter at sbml.org
• The followng SBML constructs have no meaning in xCellerator and will be ignored: units, compartmentType, speciesType.
• Level 2 Version 2 constraints and initialAssignments have not yet been implemented.

See Also:

• convertToSBML