SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.

Differences between core libSBML and extensions to libSBML

Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.

By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.

Summary of core SBML objects implemented in libSBML

Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.

SBML components and corresponding libSBML objects.
Level & Version	LibSBML container object	LibSBML data object(s)
Level 2 Version 1 and higher	ListOfFunctionDefinitions	FunctionDefinition
Level 2 Version 1 and higher	ListOfUnitDefinitions	UnitDefinition
Level 2 Versions 2–5	ListOfCompartmentTypes	CompartmentType
Level 1 and higher	ListOfCompartments	Compartment
Level 2 Versions 2–5	ListOfSpeciesTypes	SpeciesType
Level 1 and higher	ListOfSpecies	Species
Level 1 and higher	ListOfParameters	Parameter
Level 2 Version and higher	ListOfInitialAssignments	InitialAssignment
Level 1 and higher	ListOfRules	AssignmentRule, AlgebraicRule, RateRule
Level 2 Version and higher	ListOfConstraints	Constraint
Level 1 and higher	ListOfReactions	Reaction
Level 2 Version 1 and higher	ListOfEvents	Event

The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content. More...

Classes
class	libsbml.AlgebraicRule
	An SBML algebraic rule representing 0 = f(W). More...

class	libsbml.AssignmentRule
	An SBML assignment rule representing x = f(Y). More...

class	libsbml.ASTNode
	Abstract Syntax Tree (AST) representation of a mathematical expression. More...

class	libsbml.Compartment
	An SBML compartment, where species are located. More...

class	libsbml.CompartmentType
	A compartment type in SBML Level 2. More...

class	libsbml.Constraint
	An SBML constraint, for stating validity assumptions. More...

class	libsbml.ConversionOption
	A single configuration setting for an SBML converter. More...

class	libsbml.ConversionProperties
	Set of configuration option values for a converter. More...

class	libsbml.CVTerm
	A MIRIAM-compliant controlled vocabulary term. More...

class	libsbml.Date
	A MIRIAM-compliant date representation. More...

class	libsbml.DefinitionURLRegistry
	Registry of all libSBML SBML DefinitionURLs. More...

class	libsbml.Delay
	A delay on the time of execution of an SBML event. More...

class	libsbml.ElementFilter
	Base class for filter functions. More...

class	libsbml.Event
	A discontinuous SBML event. More...

class	libsbml.EventAssignment
	An assignment to a variable by an SBML event. More...

class	libsbml.FunctionDefinition
	A user-defined function in an SBML model. More...

class	libsbml.InitialAssignment
	An SBML initial assignment, evaluated once only. More...

class	libsbml.KineticLaw
	The rate expression for an SBML reaction. More...

class	libsbml.L3ParserSettings
	Controls the behavior of the Level 3 formula parser. More...

class	libsbml.ListOf
	Parent class for libSBML's 'ListOfXYZ' classes. More...

class	libsbml.ListOfCompartments
	A list of Compartment objects. More...

class	libsbml.ListOfCompartmentTypes
	A list of CompartmentType objects. More...

class	libsbml.ListOfConstraints
	A list of Constraint objects. More...

class	libsbml.ListOfEventAssignments
	A list of EventAssignment objects. More...

class	libsbml.ListOfEvents
	A list of Event objects. More...

class	libsbml.ListOfFunctionDefinitions
	A list of FunctionDefinition objects. More...

class	libsbml.ListOfInitialAssignments
	A list of InitialAssignment objects. More...

class	libsbml.ListOfLocalParameters
	A list of LocalParameter objects. More...

class	libsbml.ListOfParameters
	A list of Parameter objects. More...

class	libsbml.ListOfReactions
	A list of Reaction objects. More...

class	libsbml.ListOfRules
	A list of Rule objects. More...

class	libsbml.ListOfSpecies
	A list of Species objects. More...

class	libsbml.ListOfSpeciesReferences
	A list of SpeciesReference objects. More...

class	libsbml.ListOfSpeciesTypes
	A list of SpeciesType objects. More...

class	libsbml.ListOfUnitDefinitions
	A list of UnitDefinition objects. More...

class	libsbml.ListOfUnits
	A list of Unit objects. More...

class	libsbml.LocalParameter
	A parameter inside an SBML reaction definition. More...

class	libsbml.Model
	An SBML model. More...

class	libsbml.ModelCreator
	MIRIAM-compliant data about a model's creator. More...

class	libsbml.ModelHistory
	MIRIAM-compliant data about a model's history. More...

class	libsbml.ModifierSpeciesReference
	A reference to an SBML modifier species. More...

class	libsbml.Parameter
	An SBML parameter: a named symbol with a value. More...

class	libsbml.Priority
	The priority of execution of an SBML event. More...

class	libsbml.RateRule
	An SBML rate rule representing dx/dt = f(Y). More...

class	libsbml.RDFAnnotationParser
	MIRIAM-compliant RDF annotation reader/writer. More...

class	libsbml.Reaction
	An SBML reaction between species in an SBML model. More...

class	libsbml.RenderPkgNamespaces
	Set of SBML Level + Version + namespace triples. More...

class	libsbml.Rule
	Parent class for SBML rules in libSBML. More...

class	libsbml.SBase
	SBML's SBase class, base class of most SBML objects. More...

class	libsbml.SBasePlugin
	Base class for extending SBML objects in packages. More...

class	libsbml.SBMLConverter
	Base class for SBML converters. More...

class	libsbml.SBMLConverterRegistry
	Registry of all libSBML SBML converters. More...

class	libsbml.SBMLDocument
	Overall SBML container object. More...

class	libsbml.SBMLDocumentPlugin
	Base class for extending SBMLDocument in packages. More...

class	libsbml.SBMLError
	An error, warning or other diagnostic. More...

class	libsbml.SBMLErrorLog
	Log of diagnostics reported during processing. More...

class	libsbml.SBMLExtension
	Base class for SBML Level 3 package plug-ins. More...

class	libsbml.SBMLExtensionException
	Exception used by package extensions More...

class	libsbml.SBMLExtensionRegistry
	Registry where package extensions are registered. More...

class	libsbml.SBMLFunctionDefinitionConverter
	Converter to expand user-defined functions in-line. More...

class	libsbml.SBMLIdConverter
	Converter for replacing object identifiers. More...

class	libsbml.SBMLInferUnitsConverter
	Converter for inferring and setting parameter units. More...

class	libsbml.SBMLInitialAssignmentConverter
	Converter that removes SBML initial assignments. More...

class	libsbml.SBMLLevel1Version1Converter
	Whole-document SBML Level/Version converter. More...

class	libsbml.SBMLLevelVersionConverter
	Whole-document SBML Level/Version converter. More...

class	libsbml.SBMLLocalParameterConverter
	Converter to turn local parameters into global ones. More...

class	libsbml.SBMLNamespaces
	Set of SBML Level + Version + namespace triples. More...

class	libsbml.SBMLReactionConverter
	Converter to replace reactions with SBML rate rules. More...

class	SBMLReader
	File and text-string SBML reader. More...

class	libsbml.SBMLReader
	File and text-string SBML reader. More...

class	libsbml.SBMLRuleConverter
	Converter that sorts SBML rules and assignments. More...

class	libsbml.SBMLStripPackageConverter
	Converter that removes SBML Level 3 packages. More...

class	libsbml.SBMLUnitsConverter
	Converts a model's existing units to SI units. More...

class	libsbml.SBMLValidator
	Base class for SBML validators. More...

class	SBMLWriter
	File and text-string SBML writer. More...

class	libsbml.SBMLWriter
	File and text-string SBML writer. More...

class	libsbml.SBO
	Facilities for using the Systems Biology Ontology. More...

class	libsbml.SimpleSpeciesReference
	Abstract class for references to species in reactions. More...

class	libsbml.Species
	An SBML species – a pool of entities. More...

class	libsbml.SpeciesReference
	A reference to an SBML species in a reaction. More...

class	libsbml.SpeciesType
	A species type in SBML Level 2. More...

class	libsbml.StoichiometryMath
	Stochiometry expressions in SBML Level 2 reactions. More...

class	libsbml.SyntaxChecker
	Methods for checking the validity of SBML identifiers. More...

class	libsbml.Trigger
	The trigger expression for an SBML event. More...

class	libsbml.Unit
	A single unit referenced in an SBML unit definition. More...

class	libsbml.UnitDefinition
	A definition of a unit used in an SBML model. More...

class	libsbml.XMLAttributes
	A list of attributes on an XML element. More...

class	libsbml.XMLError
	XML-level errors, warnings and other diagnostics. More...

class	libsbml.XMLErrorLog
	Log of diagnostics reported during XML processing. More...

class	libsbml.XMLInputStream
	An interface to an XML input stream. More...

class	libsbml.XMLNamespaces
	An XML Namespace. More...

class	libsbml.XMLNode
	A node in libSBML's XML document tree. More...

class	libsbml.XMLOutputStream
	Interface to an XML output stream. More...

class	libsbml.XMLToken
	A token in an XML stream. More...

class	libsbml.XMLTriple
	A qualified XML name. More...

Functions
def	libsbml.RenderPkgNamespaces.__init__ (self, args)

Detailed Description

SBML Level 3 introduced a modular architecture, in which SBML Level 3 Core is usable in its own right (much like SBML Levels 1 and 2 before it), and optional SBML Level 3 Packages add features to this Core. To support this architecture, libSBML is itself divided into a core libSBML and optional extensions.

Differences between core libSBML and extensions to libSBML

Core libSBML corresponds to the features of SBML Levels 1 to 3 Core; they are always available, and require applications to understand only the SBML core specifications. The classes listed on the rest of this page constitute libSBML's implementation of SBML Levels 1–3, without any SBML Level 3 packages.

By contrast, the libSBML extensions are plug-ins that each implement support for a given SBML Level 3 package. Separate pages of this API manual describe the libSBML extensions for those SBML Level 3 packages that are supported at this time. They are grouped under the section titled Level 3 Extensions. The stable releases of libSBML only include extensions for officially-released package specifications; additional, experimental extensions may be available for other Level 3 packages that may not yet have been finalized by the SBML community. You can find copies of these experimental extensions at the download site for libSBML on SourceForge.net.

Summary of core SBML objects implemented in libSBML

Each type of component in a plain SBML model (i.e., one that does not use any SBML packages) is described using a specific type of SBML data object that organizes the relevant information. The top level of an SBML model definition consists of lists of these components, with every list being optional. The next table enumerates the lists and objects defined by core SBML; also shown are the SBML Level+Version combinations for which they are valid.

SBML components and corresponding libSBML objects.
Level & Version	LibSBML container object	LibSBML data object(s)
Level 2 Version 1 and higher	ListOfFunctionDefinitions	FunctionDefinition
Level 2 Version 1 and higher	ListOfUnitDefinitions	UnitDefinition
Level 2 Versions 2–5	ListOfCompartmentTypes	CompartmentType
Level 1 and higher	ListOfCompartments	Compartment
Level 2 Versions 2–5	ListOfSpeciesTypes	SpeciesType
Level 1 and higher	ListOfSpecies	Species
Level 1 and higher	ListOfParameters	Parameter
Level 2 Version and higher	ListOfInitialAssignments	InitialAssignment
Level 1 and higher	ListOfRules	AssignmentRule, AlgebraicRule, RateRule
Level 2 Version and higher	ListOfConstraints	Constraint
Level 1 and higher	ListOfReactions	Reaction
Level 2 Version 1 and higher	ListOfEvents	Event

The list of classes below constitutes the public API of core libSBML. The list includes classes that are not defined in any SBML specification; these utility classes are provided by libSBML to implement various kinds of functionality useful in the context of working with SBML content.

Function Documentation

def libsbml.RenderPkgNamespaces.__init__	(	self,
		args
	)

__init__(SBMLExtensionNamespaces<(RenderExtension)> self, long  level, long  version, long  pkgVersion, string prefix)   RenderPkgNamespaces
__init__(SBMLExtensionNamespaces<(RenderExtension)> self, long  level, long  version, long  pkgVersion)   RenderPkgNamespaces
__init__(SBMLExtensionNamespaces<(RenderExtension)> self, long  level, long  version)   RenderPkgNamespaces
__init__(SBMLExtensionNamespaces<(RenderExtension)> self, long  level)   RenderPkgNamespaces
__init__(SBMLExtensionNamespaces<(RenderExtension)> self)   RenderPkgNamespaces
__init__(SBMLExtensionNamespaces<(RenderExtension)> self, RenderPkgNamespaces orig)   RenderPkgNamespaces

Set of SBML Level + Version + namespace triples.

This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.

SBMLExtensionNamespaces is a template class. It is extended from SBMLNamespaces and is meant to be used by package extensions to store the SBML Level, Version within a Level, and package version of the SBML Level 3 package implemented by a libSBML package extension.

Basic principles of SBML package extensions in libSBML

: SBML Level 3's package structure permits modular extensions to the core SBML format. In libSBML, support for SBML Level 3 packages is provided through optional package extensions that can be plugged into libSBML at the time it is built/compiled. Users of libSBML can thus choose which extensions are enabled in their software applications.

LibSBML defines a number of classes that developers of package extensions can use to implement support for an SBML Level 3 package. These classes make it easier to extend libSBML objects with new attributes and/or subobjects as needed by a particular Level 3 package. Three overall categories of classes make up libSBML's facilities for implementing package extensions. There are (1) classes that serve as base classes meant to be subclassed, (2) template classes meant to be instantiated rather than subclassed, and (3) support classes that provide utility features. A given package implementation for libSBML will take the form of code using these and other libSBML classes, placed in a subdirectory of src/sbml/packages/.

The basic libSBML distribution includes a number of package extensions implementing support for officially-endorsed SBML Level 3 packages; among these are Flux Balance Constraints ('fbc'), Hierarchical Model Composition ('comp'), Layout ('layout'), and Qualitative Models ('qual'). They can serve as working examples for developers working to implement other packages.

Extensions in libSBML can currently only be implemented in C++ or C; there is no mechanism to implement them first in languages such as Java or Python. However, once implemented in C++ or C, language interfaces can be generated semi-automatically using the framework in place in libSBML. (The approach is based on using SWIG and facilities in libSBML's build system.)

Differences between core libSBML and extensions to libSBML

Summary of core SBML objects implemented in libSBML

Classes

Functions

Detailed Description

Differences between core libSBML and extensions to libSBML

Summary of core SBML objects implemented in libSBML

Function Documentation

Basic principles of SBML package extensions in libSBML