An answer to the question: What is a compartment?

In most cases, a compartment is a chemical species in a physical place. So neither "glucose" nor "cAMP" is a compartment, and neither "central venous blood" nor "the lumen of the rough endoplasmic reticulum" is a compartment in the sense generally used by kineticists.

Ca2+ in the cytosol and plasma insulin, on the other hand, are both compartments. In the first case Ca2+ is the chemical species and cytosol is the physical place. In the second case, insulin is the chemical species, and plasma is the physical place.

Almost always, each compartment in a model will have an associated differential equation which describes the processes capable of increasing or decreasing the amount of the chemical species in the physical place.

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