A The Bio-PEPA plugin syntax
This is a brief overview of the basic elements of the Bio-PEPA Eclipse Plug-in syntax and is by no means comprehensive. For more information on the Bio-PEPA Eclipse Plug-in syntax and its differences with Bio-PEPA see [14, 11].
A biological system can be encoded as a Bio-PEPA model by way of a 6-tuple [14]:
where:
is the set of locations
is the set of species attributes
is the set of parameter definitions
is the set of functional rates
is the set of species components
is the model component
The following sections will explain this definition by describing its constituent elements in more detail. Sections A.7 - A.10 will offer examples of models defined using the Bio-PEPA language and the Bio-PEPA Eclipse Plug-in syntax.