docs/libsbml.md

In a-kramer/SBtabVFGEN: Converts from SBtab to vf,mod,[sbml]

Useful Functions

This is taken from the guide on libsbml.org

Components to Address

The model components are species, parameters, reactions, compartments, unit definitions, and functions (λ expressions).

The model is written to file by

writeSBML(model, "sthsth.xml");

MathML

In General, math expressions for use in SBML can be written directly as MathML, or starting with infix notation strings which are converted to MathML.

Probably the most convenient way is to use the functions parseL3Formula and writeMathMLToString to inspect the results.

> F<-parseL3Formula("exp(-time)")
> message(writeMathMLToString(F))

like this:

<?xml version="1.0" encoding="UTF-8"?>
<math xmlns="http://www.w3.org/1998/Math/MathML">
  <apply>
    <exp/>
    <apply>
      <minus/>
      <csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>
    </apply>
  </apply>
</math>

The function parseL3Formula is hard to replace, very useful. Most of the sbml file could be written without using libsbml (using normal print functions [it would get tedious]), but converting infix math strings to SBML conformant MathML is not trivial to say the least (so this functions carries most of the weight here).

The reverse of parseFormula

This is pribably a rare case, but a formula given in MathML can also be used directly, given a file with MathML content ```xml formula.xml <?xml version="1.0" encoding="UTF-8"?> k1 x1 x2

a formula object can be created via:
```R
> formula.xml<-paste0(readLines("formula.xml"),collapse="\n")
> F<-readMathMLFromString(formula.xml)
> formulaToString(F)
[1] "k1 * x1 * x2"

Legacy Functions

NOTE: Formulae should probably be parsed exclusively using parseL3Formula() because it correctly detects the time variable, the older parseFormula does not:

|parse function|input|output| |-------------:|:---:|:-----| |parseFormula|"time"|<ci> time </ci>| |parseL3Formula|"time"|<csymbol encoding="text" definitionURL="http://www.sbml.org/sbml/symbols/time"> time </csymbol>|

Unit Definitions

unitdef <- Model_createUnitDefinition(model);
UnitDefinition_setId(unitdef,id);
for (i in 1:n){
 u <- UnitDefinition_createUnit(unitdef);
 Kind <- switch(unit$kind[i],
                litre="UNIT_KIND_LITRE",
                metre="UNIT_KIND_METRE",
                second="UNIT_KIND_SECOND",
                mole="UNIT_KIND_MOLE",
                gram="UNIT_KIND_GRAM",
                "UNIT_KIND_DIMENSIONLESS")
 Unit_setKind(u, Kind);
 Unit_setExponent(u,unit$exponent[i]);
 Unit_setMultiplier(u,unit$multiplier[i]);
 Unit_setScale(u,unit$scale[i]);
}

Default units are set by defining units with the special ids:

• time
• substance
• volume
• area
• length

Compartments

comp <- Model_createCompartment(model);
Compartment_setId(comp, compName);
Compartment_setSize(comp, 1);

Species (Molecules and Complexes of Molecules)

sp <- Model_createSpecies(model);
Species_setUnits(sp, SubstanceUnitID)
Species_setId(sp, "S2");
Species_setCompartment(sp, compName);
Species_setInitialConcentration(sp, 0);

where SubstanceUnitID is a string identifier of a unit definition.

Expressions

SBML has no entity that exactly matches an Expression role. We have to convert them into species, or parameters (maybe even compartments)

The difference is that simulators treat parameters and species as arguments to the model, say y'=f(y,p), but expressions are supposed to be model internal values (autonomous).

libsbml provides these functions to make AssignmentRules:

rule <- Model_createAssignmentRule(sbml)
astMath <- parseFormula(Expression$Formula[i]);
Rule_setFormula(rule, astMath)

Parameters

para <- Model_createParameter(model);
Parameter_setId(para, "t");
Parameter_setValue(para, 1);
Parameter_setUnits(para, "second");

Reactions

reaction <- Model_createReaction(model);
Reaction_setId(reaction, "reaction_1");
Reaction_setReversible(reaction, 0);

kl = Reaction_createKineticLaw(reaction);
astMath <- parseFormula(MathString); # or: readMathMLFromString(mathXMLString);
KineticLaw_setMath(kl, astMath);

a-kramer/SBtabVFGEN documentation built on Nov. 14, 2024, 8:41 p.m.