References¶

sbmlutils implements the specifications of the Systems Biology Markup Language. These are the publications behind the language and behind the packages the library supports; cite them when you describe a model, and cite sbmlutils itself as described in Home.

SBML¶

SBML Level 3. The format and the package mechanism which the whole library builds on.

Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 2020 Aug;16(8):e9110. doi:10.15252/msb.20199110 · PMID: 32845085 · PMCID: PMC8411907

SBML Level 3 Version 2 Core. The language specification itself, i.e., what a compartment, a species, a reaction, a rule and an event mean. See Model creation.

Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics. 2019 Jun 20;16(2):20190021. doi:10.1515/jib-2019-0021 · PMID: 31219795 · PMCID: PMC6798823

SBML packages¶

Flux balance constraints (fbc), version 3. Flux bounds, objectives, gene products and user defined constraints. See Flux balance constraints.

Olivier BG, Bergmann FT, Keating S, König M. SBML level 3 package: flux balance constraints version 3. Journal of Integrative Bioinformatics. 2026 Aug 13. Epub ahead of print. doi:10.1515/jib-2026-0006 · PMID: 42590802

Distributions (distrib), version 1. Uncertainties on an element and distributions in a formula. See Distributions and uncertainties.

Smith LP, Moodie SL, Bergmann FT, Gillespie C, Keating SM, König M, Myers CJ, Swat MJ, Wilkinson DJ, Hucka M. Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. Journal of Integrative Bioinformatics. 2020 Jul 20;17(2-3):20200018. doi:10.1515/jib-2020-0018 · PMID: 32750035 · PMCID: PMC7756622

Specifications¶

The current specifications of the language and of every package are published at sbml.org/documents/specifications, including the packages sbmlutils supports beyond the ones above: comp for model composition and layout for the layout information of a model.