Rate Rules

Rate Rules allow a user to define the rate of change of a variable (species) using a specified function, rather than describing a kinetic law in the reaction editor. This is convenient for many ODE applications, and is also used in many SBML models that are imported into VCell.

The functional form of a Rate Rule is dx/dt = f(W) (left hand side is a rate of change) where x is the variable, f is an arbitrary function returning a numerical result and W is a vector of symbols that may include x.

The variable cannot be a reactant or product species already defined in the reaction network, where the math will be defined by the kinetic rate law as part of the reaction diagram. Rather, a rate rule expression defines the rate of change of a variable that can act to catalyze a reaction.

The Rate Rules screen is a table with four columns.

Name is a user defined name for the rule.
The Variable is the user defined species variable whose rate of change (dx/dt) will be determined by the rate rule expression. In general the variable should not be a species already described in the reaction network or a predefined variable or constant in VCell.
Type defines the variable Type and cannot be edited. In VCell, a new "species" is created in the math description for the variable, and the value of the variable will be reported in the results as a species concentration.
Expression is the expression that will be evaluated for define the value of the variable (species).

Create a new Rate Rule using the New button at the top of the Rate Rules window.

Edit the Rate Rule by double clicking within the appropriate column. The user must choose (select from a list) a species for the Variable and enter an appropriate Expression for the rate of change.

The Name of the Rate Rule can also be edited.

The Specifications / Species panel has an extra "Rules" column for non-spatial deterministic applications, where we indicate if a species is being used as a rule variable.

In the example above, species 'e' is marked with the rate rule icon.