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UserDefinedConstraint

A constraint over a combination of fluxes and parameters, added in Version 3.

The bounds of a reaction constrain one flux at a time, and the stoichiometry of the network constrains the fluxes which share a species. A user defined constraint is everything else a modeller knows: that two reactions run at a fixed ratio, that a set of reactions shares a budget, or that a flux is coupled to a parameter which a simulation changes.

It is a sum of its components, each of which weighs one model variable, and the sum has to stay between the values of the two parameters it names as its bounds.

The report shows the user defined constraints of a model in a section of their own, with the table of their components.

Attributes

attribute type required meaning specification
lowerBound SIdRef required the parameter which holds the smallest value the constraint may take fbc v3 3.14
upperBound SIdRef required the parameter which holds the largest value the constraint may take fbc v3 3.14
listOfUserDefinedConstraintComponents list required the weighted variables the constraint is the sum of fbc v3 3.15

Every element of a model also carries the common attributes of SBase.

lowerBound

The attribute is required and names a parameter of the model, the way the lower flux bound of a reaction does, so that a scenario is changed in one place. A constraint whose two bounds name the same parameter is an equality.

  • 2021405 (error): The value of the attribute 'fbc:lowerBound' of an <userDefinedConstraint> object must be the identifier of an existing <parameter> object defined in the enclosing <model> object.

upperBound

The attribute is required and names a parameter of the model. Together with the lower bound it reads lowerBound <= sum of the components <= upperBound.

  • 2021406 (error): The value of the attribute 'fbc:upperBound' of an <userDefinedConstraint> object must be the identifier of an existing <parameter> object defined in the enclosing <model> object.

listOfUserDefinedConstraintComponents

A constraint which is defined has at least one component. The report shows them as a table of the variable, the coefficient and the type of every term, with a link to each of them.

  • 2021404 (error): An <userDefinedConstraint> object must contain one and only one instance of the <listOfUserDefinedConstraintComponents> element. No other elements from the SBML Level 3 Flux Balance Constraints namespaces are permitted on an <userDefinedConstraint> object.
  • 2021408 (error): Apart from the general notes and annotations subobjects permitted on all SBML objects, a <listOfUserDefinedConstraintComponents> container object may only contain <userDefinedConstraintComponent> objects.

Validation rules

  • 2021401 (error): An <userDefinedConstraint> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespaces are permitted on an <userDefinedConstraint>.
  • 2021402 (error): An <userDefinedConstraint> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespaces are permitted on an <userDefinedConstraint>.
  • 2021403 (error): An <userDefinedConstraint> object must have the required attributes 'fbc:lowerBound' and 'fbc:upperBound', and may have the optional attributes 'fbc:id' and 'fbc:name'. No other attributes from the SBML Level 3 Flux Balance Constraints namespaces are permitted on an <userDefinedConstraint> object.
  • 2021404 (error): An <userDefinedConstraint> object must contain one and only one instance of the <listOfUserDefinedConstraintComponents> element. No other elements from the SBML Level 3 Flux Balance Constraints namespaces are permitted on an <userDefinedConstraint> object.

Specification

SBML Level 3 Package: Flux Balance Constraints, Version 3 Release 1, Section 3.14 (Olivier and Bergmann, COMBINE specification).