Skip to content

References

The prose of this documentation is written from these sources and cites them.

  • Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. SBML Level 3 Version 2 Core, Release 2. Journal of Integrative Bioinformatics. 2019;16(2):20190021. doi:10.1515/jib-2019-0021
  • Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, et al. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology. 2020;16(8):e9110. doi:10.15252/msb.20199110
  • Smith LP, et al. SBML Level 3 Package: Hierarchical Model Composition, Version 1 Release 3. Journal of Integrative Bioinformatics. 2015;12(2):268. doi:10.2390/biecoll-jib-2015-268. Specification
  • Olivier BG, Bergmann FT. SBML Level 3 Package: Flux Balance Constraints, Version 2 Release 1. Journal of Integrative Bioinformatics. 2018;15(1):20170082. doi:10.1515/jib-2017-0082. Specification
  • Olivier BG, Bergmann FT. SBML Level 3 Package: Flux Balance Constraints, Version 1 Release 1. 2013. Specification, the version whose flux bounds are objects of the model
  • Olivier BG, Bergmann FT. SBML Level 3 Package: Flux Balance Constraints, Version 3 Release 1. Specification, the version the report reads the gene associations, the user defined constraints and the key value pairs from
  • Chaouiya C, et al. SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology. 2013;7:135. doi:10.1186/1752-0509-7-135. Specification
  • Smith LP, et al. The Distributions Package for SBML Level 3, Version 1 Release 1. Journal of Integrative Bioinformatics. 2020;17(2-3):20200018. doi:10.1515/jib-2020-0018. Specification
  • Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnology. 2005;23:1509-1515. doi:10.1038/nbt1156
  • Systems Biology Ontology (SBO). www.ebi.ac.uk/ols4/ontologies/sbo
  • identifiers.org, the registry of resolvable identifiers for life science data. registry.identifiers.org
  • COMBINE archive specification. co.mbine.org/standards/omex
  • Das S. Interactive SBML report for Humans (SBML4Humans), Google Summer of Code 2021 project, mentored by Matthias König and Ralf Steuer. NRNB GoogleSummerOfCode issue nrnb/GoogleSummerOfCode#164 and the project blog sbml4humans-gsoc-2021.blogspot.com