CellDesigner Help

Compartment in SBML

SBML (Level 2 Version 4) specification defines a compartment as follows:

A compartment in SBML represents a bounded space in which species are located. Compartments do not necessarily have to correspond to actual structures inside or outside of a biological cell, although models are often designed that way.

Compartment in CellDesigner

In CellDesigner, there is a distinction between the terms Compartment and CompartmentAlias.

Compartment is identical to the compartment in SBML definition. It is simply a logical entity and does not have any graphical information.

CompartmentAlias is a graphical representaion of a relevant Compartment.

So, when you create a Compartment, the graphic object you draw on canvas is in fact a CompartmentAlias, and not a Compartment.

Various CompartmentAliases

If a new Compartment is created and given the same name as the existing Compartment, it will be regarded as the second CompartmentAlias of the same Compartment. Compartment is identified and distinguished only by its name, not by its shape.

Different CompartmentAliases having the same name belong to the same Compartment.