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.
Hierarchical Model Composition package, Version 1 Release 3
Errata page
