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BY 4.0 license Open Access Published by De Gruyter July 20, 2020

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

Lucian P. Smith ORCID logo EMAIL logo , Stuart L. Moodie ORCID logo , Frank T. Bergmann ORCID logo , Colin Gillespie ORCID logo , Sarah M. Keating ORCID logo , Matthias König ORCID logo , Chris J. Myers ORCID logo , Maciek J. Swat , Darren J. Wilkinson ORCID logo and Michael Hucka ORCID logo

Abstract

Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.


Corresponding author: Lucian P. Smith, University of Washington, Seattle, USA, E-mail:

Funding source: National Institute of General Medical Sciences (NIGMS, US)

Award Identifier / Grant number: R01-GM070923

Funding source: Federal Ministry of Education and Research (BMBF, Germany) within the research network Systems Medicine of the Liver (LiSyM)

Award Identifier / Grant number: 031L0054

Funding source: German Federal Ministry of Education and Research

Award Identifier / Grant number: FKZ: 031L0104A

Received: 2020-04-04
Accepted: 2020-04-17
Published Online: 2020-07-20

© 2020 Lucian P. Smith et al., published by De Gruyter, Berlin/Boston

This work is licensed under the Creative Commons Attribution 4.0 International License.

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