The model also contains a list of global quantities. Roughly speaking the global quantities can be used to describe values that are not necessarily a concentration or a volume. But to be more specific: The global quantities can have three different modes (called "types" in the GUI).
"Fixed" quantities always take a constant value. While the GUI still displays an initial value and a transient value those are always the same. This can be used if the same numerical value is used in several parts of the model (e.g. several reactions use a common kinetic parameter) but you want to be able to change this value in a single place.
Quantities with assignment
Global quantities can also have an assignment rule. This means a mathematical expression is specified (which can involve other variable or constant values from the model) and the value of the global quantity is alway the value of this expression. Circular definitions are not allowed. Global quantities with assignment do not have an initial value (since their value is always, also at the beginning of a simulation, determined by the mathematical expression). These assigned quantities could be used for output only (e.g. if you want to plot the sum of some concentrations) or can be used in the model itself.
Quantities with ordinary differential equation
If global quantities are set to the "ode" mode they become true variables of the model. A mathematical expression has to be specified and this expression is interpreted as the right hand side of an ordinary differential equation for this variable. An initial value has to be provided for these quantities.
Since there is no obvious probabilistic interpretation of a general ode stochastic simulation is currently disabled for models containing global quantities of type "ode".