The Bio-PEPA Eclipse Plug-inUser Manual: Species Attributes

A.2 Species Attributes

The concrete syntax for the species attributes, as accepted by the plug-in is as follows [14]:

$\begin{array}{r} \mathsf{species} \; speciesID : \mathsf{upper} = value \; \langle , \; \mathsf{lower} = value \rangle ; \end{array}$

where $speciesID$ is one of the following [14]:

$\mathbf{speciesID}$ Referring to just the species identifier is seen as a global reference. If a species can exist in three locations and a reaction is stated in terms of the species, then the reaction is assumed to be defined as occurring in all three locations independently of each other.
$\mathbf{speciesID@locationID}$ This allows a reference to a specific species in a specific location. If a reaction is defined in this manner it will not be enabled in other locations that the species can exist in.
$\mathbf{speciesID@locID_1 ,. . . ,locID_ n}$ If a reference to a species in more than one location, but not all, is required then a comma delimited list can be used. This allows fine-grained control over where the definition in question is applicable.

The only required attribute in the definition is the upper bound ( $value \in N^{\star }$ ), as the default lower bound is the value zero. If an improved lower bound is known then it can also be specified ( $value \in N^{\star }$ ) [14].

Some examples of species attribute definition for a species $S$ follow:

`species S`	`:`	`upper = 40, lower = 10;`
`species S@main`	`:`	`upper = 40, lower = 10;`
`species S@main,child`	`:`	`upper = 40, lower = 10;`

In the first definition species $S$ is defined globally, while in the following definitions it is defined in specific locations (S@main, S@main,child).