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FluxBound

A constraint on the flux of a reaction, as fbc Version 1 writes it.

A flux bound of the first version of the package is an object of the model which names a reaction, an operation and a value, so that two of them are needed to keep a flux inside an interval and one with the operation equal fixes it.

Version 2 removed the construct: a reaction names the parameters of its lower and its upper bound instead, which lets other elements of the model compute a bound and keeps one bound in one place for many reactions. The report shows a flux bound only for a document which is written in Version 1, where it is the only place the capacity of a reaction is stated.

Attributes

attribute type required meaning specification
reaction SIdRef required the reaction whose flux the bound constrains fbc v1 3.5
operation FbcOperation required how the flux is related to the value: greaterEqual, lessEqual or equal fbc v1 3.2.2
value double required the number the flux is compared with fbc v1 3.5

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

reaction

The attribute is required and names a reaction of the model. The report links it, and the inspector of the reaction lists every bound which constrains it under "referenced by", which is where the capacity of a reaction of a Version 1 model is read.

  • 2020404 (error): The attribute 'fbc:reaction' of a <fluxBound> must be of the data type SIdRef.
  • 2020408 (error): The value of the attribute 'fbc:reaction' of a <fluxBound> object must be the identifier of an existing <reaction> object defined in the enclosing <model> object.
  • 2020409 (error): The combined set of all <fluxBound>'s with identical values for 'fbc:reaction' must be consistent. That is while it is possible to define a lower and an upper bound for a reaction, it is not possible to define multiple lower or upper bounds.

operation

The operation says which side of the value the flux has to stay on. greaterEqual and lessEqual are the lower and the upper bound, equal fixes the flux at the value, which is how a measured exchange rate is written.

The report shows the operation next to the value.

  • 2020406 (error): The attribute 'fbc:operation' of a <fluxBound> must be of the data type FbcOperation and thus it's value must be one of 'lessEqual', 'greaterEqual' or 'equal'.
  • 2020409 (error): The combined set of all <fluxBound>'s with identical values for 'fbc:reaction' must be consistent. That is while it is possible to define a lower and an upper bound for a reaction, it is not possible to define multiple lower or upper bounds.

value

The value carries the units of a reaction flux, extent per time, which the model defines globally. An infinite value states that the flux is not bounded in that direction, and the report shows it as the sign of infinity with the direction of that bound.

  • 2020407 (error): The attribute 'fbc:value' of a <fluxBound> must be of the data type double.

Validation rules

  • 2010301 (error): (Extends validation rule #10301 in the SBML Level 3 Version 1 Core specification.) Within a <model> object the values of the attributes id and fbc:id on every instance of the following classes of objects must be unique across the set of all id and fbc:id attribute values of all such objects in a model: the model itself, plus all contained <functionDefinition>, <compartment>, <species>, <reaction>, <speciesReference>, <modifierSpeciesReference>, <event>, and <parameter> objects, plus the <fluxBound>, <objective>, <fluxObjective>, <geneProduct> and <geneProductAssociation> objects defined by the Flux Balance Constraints package.
  • 2020401 (error): A <fluxBound> object may have the optional SBML Level 3 Core attributes 'metaid' and 'sboTerm'. No other attributes from the SBML Level 3 Core namespace are permitted on a <fluxBound>.
  • 2020402 (error): A <fluxBound> object may have the optional SBML Level 3 Core subobjects for notes and annotations. No other elements from the SBML Level 3 Core namespace are permitted on a <fluxBound>.
  • 2020403 (error): A <fluxBound> object must have the required attributes 'fbc:reaction', 'fbc:operation' and 'fbc:value', and may have the optional attributes 'fbc:id' and 'fbc:name'. No other attributes from the SBML Level 3 Flux Balance Constraints namespace are permitted on a <fluxBound> object.

Specification

SBML Level 3 Package: Flux Balance Constraints, Version 1 Release 1, Section 3.5 (Olivier and Bergmann 2013, COMBINE specification).