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BY-NC-ND 4.0 license Open Access Published by De Gruyter April 26, 2018

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

Michael Hucka , Frank T. Bergmann ORCID logo , Andreas Dräger ORCID logo , Stefan Hoops , Sarah M. Keating ORCID logo , Nicolas Le Novère ORCID logo , Chris J. Myers ORCID logo , Brett G. Olivier ORCID logo , Sven Sahle , James C. Schaff , Lucian P. Smith ORCID logo EMAIL logo , Dagmar Waltemath ORCID logo and Darren J. Wilkinson ORCID logo

Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

Keywords: SBML; modeling; standards
Received: 2017-12-19
Revised: 2018-2-2
Accepted: 2018-2-2
Published Online: 2018-4-26

©2018 Michael Hucka et al., published by De Gruyter

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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