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SBMLRead Options

Return Value  |   Options  |   Variable Names and Scoping  |   Examples
Option Value Description
concise True Turn off verbose listing. Opposite of verbose.
context Automatic

Context to use for model. See below for a description of contexts in SBMLRead.

Context -> Automatic means generate context from the name (level 1) or id (level 2) of the model in the XML file.

Context -> None means place all variables in the Global` context. Note that if variables are placed in the Global` context then a clash with global or default Mathematica variables may occur, for example, the variables E and Pi, if they occur in the model, will be treated as the constants 2.718 ... and 3.14 ..., etc.

defaultICIndeterminateValue to be used for initial conditions of variables when that are not assigned initial conditions in the model.
defaultParameterValueIndeterminateValue to be used for parameters that are not assigned values inthe model.
evaluateParametersTrueImmediately evaluate all parameters before returning the model. Otherwise all parameters are returned in their symbolic form.
returnsee belowDetermines what gets returned by SBMLRead, as described below.
PlotOptions {}

If PlotOptions -> {} then automatic plotting will be inhibited.

If Plot Options->True then if automatic numerical solution was requeseted, it will automatically be sent to SBMLPlot.

Automatic numerical solution is controled by the return option SBMLNumericalSolution.

If PlotOptions -> a list of options, then automatic plotting will be invoked, and the options will be passed to SBMLPlot. Any valid options for SBMLPlot or Plot may be included here.

stats False Controls whether a table of statistics about the model is printed.
SBMLMassBalanceRateVector Automatic Name of the rate vector used if return → {..., SBMLMassBalanceEquations→ True,...} or as the rate constants if return→ {..., SBMLMassActionEquations → True,...}. If not specified (or specified as Automatic) a new unique variable vn for some integer n will be defined.
underscore\[UnderBracket]Character to replace underscore ( "_") in an identifier. Any valid Mathematica character may be specified.
verbose False Produce an interpretive listing. See below for additional options that control the verbose listing.

Options for return

Option Value Description
SBMLAlgebraicRules True If True, return a list of algebraic rules as the value of SBMLAlgebraicRules, if any algebraic rules exist in the model. If there are no algebraic rules in the model then a null list will be returned.
SBMLAssignmentRules True If True, return a list of assignment rules as the value of SBMLAssignmentRules, if any assignment rules exist in the model. If there are no assignment rules in the model then a null list will be returned. [new in MathSBML 2.3.20. Level 2 only.]
SBMLCompartments True If True then return a list of the compartments in the model. [new in MathSBML 2.3.10]
SBMLConstraintRules True If True, return a list of constraint rules as the value of SBMLConstraintRules. [new in MathSBML 2.4.18, Level 2 Version 2 only.]
SBMLEvents True If True, return a list of event defintions as the value of SBMLEvents. If there are no events a null list is returned. Not valid in SBML Level 1.
SBMLFunctions True If True, return a list of pure function defintions as the value of SBMLFunctions. If there are no functions then a null list will be returned. Not valid in SBML Level 1.
SBMLIC True If True, returns a list of initial condtions as the value of SBMLIC if any of the species in the model contain initial conditions or the invocation to SBMLRead sets defaultIC. If there are no initial conditions, a null list will be returned.
SBMLMassActionEquations True If True then return the mass action equations based on the stoichiometry matrix. Selection of this option forces calculation of the stoichiometry matrix. [new in MathSBML 2.4.2. Level 2 only.]
SBMLMassBalanceEquations True If True then return the mass balance equations based on the stoichiometry matrix. Selection of this option forces calculation of the stoichiometry matrix. [new in MathSBML 2.4.2. Level 2 only.]
SBMLModelName True If True, return the name (SBML Level 1) or id (Level 2) of the model as the value of SBMLModelName. If no model identifier is included in the model, an identifer is automatically generated, and its value will be given here. This value is used to set the context of the model, unless the context option is used in the call to SBMLRead.
SBMLNameIDAssociations True If True, return a list of name/id associations as the value of SBMLNameIDAssociations. If there are no name fields then a null list is returned. Not valid in SBML Level 1.
SBMLNumericalSolution 0 If set to a positive numerical value, then call SBMLNDSolve for the requested amount of time and return the list of interpolating functions thereby generated as the value of SBMLNumericalSolution. Otherwise, this field is not returned.
SBMLODES True If True, returns a list of differential equations as the value of SBMLODES, if any rules or reactions lead to differential equations in the model. If there are no differential equations, then a null list will be returned.
SBMLParameters True If True, return a list of parameter rules as the value of SBMLParameters, if there are any parameters in the model that are assigned values. If there are no such parameters in the model then a null list will be returned.
SBMLReactions True If True, and if there are any reactions in the model, return a list of reactions as the value of SBMLReactions. If there are no reactions, a null list will be returned.
SBMLSpecies True valign="top" If True, return returns a list of species names (SBML Level 1) or ids (SBML Level 2) as the value of SBMLSpecies. If there are no species in the model then a null list will be returned.
SBMLSpeciesTypes True valign="top" If True, return returns a list of species types (SBML Level 2 Version 2) as the value of SBMLSpecies. If there are no species in the model then a null list will be returned.
SBMLSpeciesTypeAssociations True valign="top" If True, return returns a list of rules associating each species with its species types (SBML Level 2 Version 2).
SBMLSpeciesCompartmentAssociations True If True then return a list {s1->c1, s2->c2, ...}. [new in MathSBML 2.3.20. Level 2 only.]
SBMLStoichiometryMatrix True If True then return the stoichiometry matrix. [new in MathSBML 2.4.2. Level 2 only.]
SBMLUnitAssociations True If True, return a list of variable/unit associations as the value of SBMLUnitAssociations. At the minimum, all species will have unit assignments, even if units are not defined or assigned explicitly in the model, because of default unit assignments.
SBMLUnitDefinitions True If True, reutrn a list of unit definitions as the value of SBMLUnitDefinitions. Default unit defintions will always be included in this list.

SBMLRead options to control the verbose listing

The options in this table are ignored unless verbose->True.

Option Value Description
align "Left" Determines alignment of data within each column. Values are "Left", "Center", "Right"
shortenODES False If True, the differential equations printed will be printed in Mathematica //Short form.
showKineticLaw True Controls whether kinetic laws for individual reactions are printed.
showReactionParameters True Controls whether the reaction listing includes a column describing local parameters.
verboseContext False Controls whether identifiers in the model are printed using their full context, as in foo`x and foo`reaction32`x (when True), or only in their shortened form, as in x (when False). Identifiers within the return value of SBMLRead will always include the full context, regardless of the value of verboseContext.
verboseStoichiometry False Prints stoichiometry matrix if it is calculated.
verboseMassActionEquations False Prints mass action equations if they are calculated.
verboseMassBalanceEquations False Prints mass balance equations if they are calculated.

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