Table 5.

Assumptions behind “traditional” rate laws, and the problems they imply for general multicompartmental modeling.

Assumption	Problem
All species that participate in a given reaction are located in one compartment	SBML must support reaction processes (e.g., transport) that move species between compartments
Compartments are three-dimensional volume containers	SBML must support models where reactions may take place at interfaces (e.g., 2-D membranes) between compartments, thus involving compartments with different dimensions
Compartment volumes are constant over time	SBML must support systems with compartments that can change size over time