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

Creators: Smith, Lucian P.; Moodie, Stuart L.; Bergmann, Frank T.; Gillespie, Colin; Keating, Sarah M.; König, Matthias; Myers, Chris J.; Swat, Maciek J.; Wilkinson, Darren J.; Hucka, Michael

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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.

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© 2020 Lucian P. Smith et al., published by De Gruyter. This work is licensed under the Creative Commons Attribution 4.0 Public License. Received April 4, 2020; accepted April 17, 2020; published online July 20, 2020. Much of the initial concrete work leading to this proposal document was carried out at the Statistical Models Workshop in Hinxton in 2011, which was organized by Nicolas Le Novère. A list of participants and recordings of the discussion is available from http://sbml.org/Events/Other_Events/statistical_models_workshop_2011. Before that a lot of the ground work was carried out by Darren Wilkinson who led the discussion on distrib at the Seattle SBML Hackathon and before that Colin Gillespie who wrote an initial proposal back in 2005. The authors would also like to thank the participants of the distrib sessions during various HARMONY and COMBINE meetings for their excellent contributions in helping revising this proposal; Sarah Keating, Maciej Swat, Nicolas Le Novère, and Matthias König for useful discussions, corrections and review comments; and Mike Hucka for LATEX advice, text editing, and the template upon which this document is based.

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