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sbmlteam / sbml-specifications

The specification documents for SBML.
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Spatial: boundaryCondition vs. BoundaryCondition #371

Closed luciansmith closed 2 years ago

luciansmith commented 2 years ago

The species attribute boundaryCondition needs to be addressed more explicitly in the spatial BoundaryCondition section, if only to clear up confusions. Reported by @jcschaff

luciansmith commented 2 years ago

New proposed text:

"The boundaryCondition attribute on an SBML core Species defines whether it is (false) or is not (true) changed by any Reaction it may appear in as a product or reactant. In a spatial context, setting this attribute to true additionally means that is will not be changed by advection, diffusion, or (confusingly) any BoundaryCondition. This is because the 'boundary' of a BoundaryCondition refers to a physical boundary, while the 'boundary' of the boundaryCondition attribute refers to the conceptual boundary of the reaction network. As in SBML Core, a Species with a boundaryCondition of true may only be changed by a Rule (AssignmentRule, RateRule, or AlgebraicRule)."