SimBiology model components include quantities and expressions. You can refer to model quantities (compartments, species, and parameters) by their names in an expression, such as a reaction or an assignment equation. Follow these guidelines when you name model components or referencing their names in expressions. When evaluating a name that matches different quantities, SimBiology resolves it by following precedence rules.
Model and parameter names cannot contain brackets
] and cannot be empty, the word
or all whitespace.
Compartment and species names cannot contain the characters
] and cannot be empty,
null, or the word
However, a name can contain the words
time within the name, such as
Reaction, event, and rule names cannot contain brackets
] and cannot be the word
If the quantity name is not a valid MATLAB® variable name, you must enclose the name in brackets when
referring to it in an expression. For example, if the name of a species
is DNA polymerase+, write
If you have multiple species with the same name in different
compartments, you must qualify the name by referring to the name of the
compartment that contains the species. For example, the qualified name
polymerase+] refers to the DNA
polymerase+ species that resides in the
If a name referenced in an expression matches multiple quantities, SimBiology evaluates the expression using precedence rules. The rules depend on whether the name is referenced in a reaction or other expressions that are not reactions.
When a reaction refers to a name that matches different quantities, SimBiology evaluates the name as the first quantity with a matching name in this order: species, parameter scoped to the reaction, compartment, or parameter scoped to the model.
There are different types of expressions that are not reactions, namely rules and events. Rules include initial and repeated assignment equations, algebraic equations, and differential rate equations. An event contains expressions that represent an event trigger and one or more event functions to model discrete transitions in the values of quantities or expressions in the model.
When a nonreaction expression refers to a name that matches different quantities, SimBiology evaluates the name as the first quantity with a matching name in this order: species, compartment, or parameter scoped to the model.