MathSBML Model Builder: speciesToSBML, speciesToSymbolicSBML

speciesToSBML[options] returns a single <species.../> definition.

speciesToSBML[{{options}, {options},...}] returns a <listOfSpecies.../> where each option list refers to a separate species.

speciesToSymbolicSBML[arguments] returns Symbolic SBML for a <species.../> definition.

Options

Experimental Options

If Arrays->True is set by an call to newModel[]: ArrayDimensions->{i->{min,max},j->{min,max},...} or {} (default).

Example 1: Single Species

The following input expression will create a single species definition (linefeeds and indentation added to emphasize syntax):

	speciesToSBML[id->"fred", 
		name->"Fred Flintstone", 
		compartment->"bedrock" , 
		boundaryCondition->"false",
		constant->"true", 
		initialConcentration->5, 
		substanceUnits->"rocks", 
		charge->17]

and will produce the following output (line feeds and indentation added to emphasize format):

	<species id="fred" 
		name="Fred Flintstone" 
		compartment="bedrock" 
		boundaryCondition="false" 
		constant="true" 
		initialConcentration="5" 
		substanceUnits="rocks" 
		charge="17"/>

Example 2: Multiple Species

The following will generate a listOfSpecies SBML fragment:

	speciesToSBML[{{id-> "fred", compartment-> "bedrock"}, 
	               {id-> "barney",compartment-> "bedrock"}
	               }]

A string containing the following SBML, including embedded line feeds and spaces for indentations, will be returned:

	<listOfSpecies>
	 <species id="fred"
	     name="fred"
	     compartment="bedrock"
	     boundaryCondition="false"
	     constant="false"
	     substanceUnits="substance"
	     hasOnlySubstanceUnits="false"/>
	 <species id="barney"
	     name="barney"
	     compartment="bedrock"
	     boundaryCondition="false"
	     constant="false"
	     substanceUnits="substance"
	     hasOnlySubstanceUnits="false"/>
	</listOfSpecies>

This page last modified 10 May 2005