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Distributions (distrib)

The package which records the uncertainty of a value.

The distrib package attaches statistical measures to the elements of a model which have a mathematical meaning: a mean, a standard deviation, a variance, a confidence interval or the distribution a value was drawn from. The measures describe the value at the moment it is computed, not how it changes during a simulation.

They do not affect the mathematics of the model. They are a controlled format for the provenance of a number, which a modeller would otherwise write into the notes of an element, and a tool may use them as it uses any other annotation.

The report shows the uncertainties of an element in its inspector and every uncertainty as an element of its own.

Validation rules

  • 1510101 (error): To conform to the Distributions Package specification for SBML Level 3 Version 1, an SBML document must declare 'http://www.sbml.org/sbml/level3/version1/distrib/version1' as the XMLNamespace to use for elements of this package.
  • 1510102 (error): Wherever they appear in an SBML document, elements and attributes from the Distributions Package must use the 'http://www.sbml.org/sbml/level3/version1/distrib/version1' namespace, declaring so either explicitly or implicitly.
  • 1520101 (error): In all SBML documents using the Distributions Package, the <sbml> object must have the 'distrib:required' attribute.
  • 1520102 (error): The value of attribute 'distrib:required' on the <sbml> object must be of data type 'boolean'.
  • 1520103 (error): The value of attribute 'distrib:required' on the <sbml> object must be set to 'true'.
  • Uncertainty: a set of statistical measures of the value of an element
  • Parameter: a named value which the mathematics of the model can use
  • Species: a pool of a chemical entity in a compartment

Specification

The Distributions Package for SBML Level 3, Version 1 Release 1 (Smith et al. 2020, J Integr Bioinform 17(2-3):20200018).