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SBML Level 3 Package Specification: Hierarchical Model Composition

Smith, Lucian P. and Hucka, Michael and Hoops, Stefan and Finney, Andrew and Ginkel, Martin and Myers, Chris J. and Moraru, Ion I. and Liebermeister, Wolfram (2013) SBML Level 3 Package Specification: Hierarchical Model Composition. SBML Level 3 Package Specification, V1 Release3. . https://resolver.caltech.edu/CaltechAUTHORS:20141028-180615369

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Abstract

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.


Item Type:Report or Paper (Documentation)
Related URLs:
URLURL TypeDescription
http://sbml.org/Special/specifications/sbml-level-3/version-1/comp/sbml-comp-version-1-release-3.pdfOrganizationThis document on sbml.org website.
http://identifiers.org/combine.specifications/sbml.level-3.version-1.comp.version-1.release-3OtherIdentifiers.org persistant URL
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Contact Email Address:lpsmith@u.washington.edu
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.
Funders:
Funding AgencyGrant Number
NIHR01 GM070923
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Series Name:SBML Level 3 Package Specification
Issue or Number:V1 Release3
Record Number:CaltechAUTHORS:20141028-180615369
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20141028-180615369
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:50975
Collection:CaltechAUTHORS
Deposited By: Linda Taddeo
Deposited On:29 Oct 2014 23:30
Last Modified:03 Oct 2019 07:28

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