Let’s go through an example. We’ll construct a model in which an
intracellular cell cycle network (ODE) regulates the division of motile cells which (CPM) release a diffusive cytokine (PDE) which, in turn, controls the cell cycle (ODE).

“What is the difference between an Equation, a Rule and a Function ?”
Both are algebraic expressions, however:
An Equation is an equality relation the simulator is expected to keep throughout simulation time.