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No outside attribute

The Level 2 specification defines the Compartment component as having an attribute outside. The attribute's purpose was to allow the expression of (very) simple position relationships. The original motivation (dating back to SBML Level 1) was to support simple drawing applications. Unfortunately, the attribute has turned out to be repeatedly misunderstood. Most often, the confusion is that models or modelers assume being "inside" means containment; for example, the idea that the volume of a compartment B includes the volume of a compartment A contained within it. (Example.) Moreover, the outside attribute is an extremely and incomplete limited mechanism for representing any real topological relationships. Finally, Level 3 will have a package that will provide a better means of defining topological relationships, and it may do so in a way that will at least duplicate (and possibly conflict with) the outside scheme as it is currently defined. For all these reasons, the outside attribute on Compartment will be removed.

Changes compared to Level 2

For the reasons given above, Level 3 Core removes the outside attribute on compartment. The new definition of the Compartment component is shown below:


(Note that this diagram also shows changes due to the removal of CompartmentType and the removal of restrictions on the spatialDimensions attribute .)

Notable implications

Since the outside attribute could not affect the mathematics or the interpretation of a model, its removal will not affect simulation and analysis of SBML models.

The removal may affect software tools that perform automatic layout of diagrams. It is hoped that the forthcoming Level 3 package for topology will address the needs of these software applications.

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This page was last modified 17:01, 11 June 2009.



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