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Published November 14, 2013 | Published
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SBML Level 3 Package Specification: Hierarchical Model Composition


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 (Hucka et al., 2010), by itself, has no direct support for allowing a model to include other models as submodels. Software tools either have to implement their own schemes outside of SBML, or (in principle) could use annotations to augment a plain SBML Level 3 model with the necessary information to allow a software tool to compose a model out of submodels. However, such solutions would be proprietary and tool-specific, and not conducive to interoperability. There is a clear need for an official SBML language facility for hierarchical model composition. This document describes a specification for an SBML Level 3 package that provides exactly such a facility.

Additional Information

We thank with great enthusiasm the National Institutes of Health (USA) for partly funding the development of this package under grant R01 GM070923, as well as the European Molecular Biology Laboratory (EMBL) for funding workshops that led to the development of this package.

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Published - sbml-comp-version-1-release-3.pdf


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