Hierarchical Model Composition

The libSBML “comp” extension implements support for the SBML Level 3 Hierarchical Model Composition package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

In the context of SBML, hierarchical model composition refers to the ability to include models as submodels inside another model. The goal is to support the ability of modelers and software tools to do such things as (1) decompose larger models into smaller ones, as a way to manage complexity; (2) incorporate multiple instances of a given model within one or more enclosing models, to avoid literal duplication of repeated elements; and (3) create libraries of reusable, tested models, much as is done in software development and other engineering fields. SBML Level 3 Version 1 Core, by itself, has no direct support for allowing a model to include other models as submodels. The Level 3 Hierarchical Model Composition package adds the missing capabilities. The figure below illustrates some of the scenarios targeted by this package.

Two examples of model configuration supported by the “comp” package: (left) a model composed of a submodel that is itself composed of submodels; (right) a model composed of submodels, one of which is defined in an external file.

Authors

The primary authors of the SBML Level 3 Hierarchical Model Composition specification are Lucian P. Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion Moraru and Wolfram Liebermeister.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Hierarchical Model Composition (“comp”) package. If you are developing software that uses “comp”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Hierarchical Model Composition, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Hierarchical Model Composition package, Version 1 Release 3	Errata page

More...

Classes
class	libsbmlcs.CompBase
	comp Convenience class for SBase-derived classes. More...
class	libsbmlcs.CompExtension
	comp Base extension class for the package. More...
class	libsbmlcs.CompFlatteningConverter
	comp 'Flattens' a model, removing composition. More...
class	libsbmlcs.CompModelPlugin
	comp Extension of Model. More...
class	libsbmlcs.CompSBasePlugin
	comp Extension of SBase. More...
class	libsbmlcs.CompSBMLDocumentPlugin
	comp Extension of SBMLDocument. More...
class	libsbmlcs.Deletion
	comp Deletion of an object from a submodel. More...
class	libsbmlcs.ExternalModelDefinition
	comp A reference to an externally-defined model. More...
class	libsbmlcs.ListOfDeletions
	comp A list of Deletion objects. More...
class	libsbmlcs.ListOfExternalModelDefinitions
	comp A list of ExternalModelDefinition objects. More...
class	libsbmlcs.ListOfModelDefinitions
	comp A list of ModelDefinition objects. More...
class	libsbmlcs.ListOfPorts
	comp A list of Port objects. More...
class	libsbmlcs.ListOfReplacedElements
	comp A list of ReplacedElement objects. More...
class	libsbmlcs.ListOfSubmodels
	comp A list of Submodel objects. More...
class	libsbmlcs.ModelDefinition
	comp A model used in model composition. More...
class	libsbmlcs.Port
	comp An interface to be used in composition. More...
class	libsbmlcs.ReplacedBy
	comp Indicates an object replaced by another. More...
class	libsbmlcs.ReplacedElement
	comp Indicates an object replaces another. More...
class	libsbmlcs.Replacing
	comp Convenience class. More...
class	libsbmlcs.SBaseRef
	comp Base class for references to objects. More...
class	libsbmlcs.SBMLFileResolver
	comp Resolves documents stored on a file system. More...
class	libsbmlcs.SBMLResolver
	comp Base class for SBML resolvers. More...
class	libsbmlcs.SBMLResolverRegistry
	comp Registry of all SBML resolvers. More...
class	libsbmlcs.SBMLUri
	comp Utility class for handling URIs. More...
class	libsbmlcs.Submodel
	comp A model instance inside another model. More...

Detailed Description

The libSBML “comp” extension implements support for the SBML Level 3 Hierarchical Model Composition package. It can be used in SBML Level 3 Version 1 and Version 2 documents.

Introduction

In the context of SBML, hierarchical model composition refers to the ability to include models as submodels inside another model. The goal is to support the ability of modelers and software tools to do such things as (1) decompose larger models into smaller ones, as a way to manage complexity; (2) incorporate multiple instances of a given model within one or more enclosing models, to avoid literal duplication of repeated elements; and (3) create libraries of reusable, tested models, much as is done in software development and other engineering fields. SBML Level 3 Version 1 Core, by itself, has no direct support for allowing a model to include other models as submodels. The Level 3 Hierarchical Model Composition package adds the missing capabilities. The figure below illustrates some of the scenarios targeted by this package.

Two examples of model configuration supported by the “comp” package: (left) a model composed of a submodel that is itself composed of submodels; (right) a model composed of submodels, one of which is defined in an external file.

Authors

The primary authors of the SBML Level 3 Hierarchical Model Composition specification are Lucian P. Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J. Myers, Ion Moraru and Wolfram Liebermeister.

The specification for this SBML package

This API documentation for libSBML does not provide a complete explanation of the SBML Level 3 Hierarchical Model Composition (“comp”) package. If you are developing software that uses “comp”, you are strongly urged to read the actual specification for the package. A link to the specification document current is provided below, along with a link to the page of known issues (if any).

Specification for SBML Level 3 Hierarchical Model Composition, current at the time of this libSBML release (5.18.0). Note: an Internet connection is required to access these documents.

Specification (in PDF format)	Known issues
Hierarchical Model Composition package, Version 1 Release 3	Errata page