10 Inference of Invariants

The Bio-PEPA Eclipse Plug-in allows you to infer invariants from your Bio-PEPA model. There are two types of invariants that can be infered from a Bio-PEPA model:

State invariants: A sum of populations in the model that remains constant. For example, in a model that contains two species $A$ and $B$ , that are involved in only two reactions $A$ $\ensuremath{\rightarrow }$ $B$ and $B$ $\ensuremath{\rightarrow }$ $A$ the sum $A+B$ is constant.
Activity invariants: A sequence of reactions that, once completed, returns the model to its initial state. For example, in the above model, the sequence of reactions $A$ $\ensuremath{\rightarrow }$ $B$ , $B$ $\ensuremath{\rightarrow }$ $A$ , leaves the model unchanged.

To perform inference of invariants for a model you should open the Invariants View by going to Window $\ensuremath{\rightarrow }$ Show View $\ensuremath{\rightarrow }$ Other (see Figure 47). Then, in the dialogue box that appears, go to Analysis $\ensuremath{\rightarrow }$ Invariants (see Figure 48) and click on the OK button.

$\includegraphics[scale=0.5]{screenshots/screenshots/infer_invariants_view1}$

Figure 64: Opening a view

$\includegraphics[scale=0.5]{screenshots/screenshots/infer_invariants_view2}$

Figure 65: Opening the Invariants View

In order to present this option of the Bio-PEPA Eclipse Plug-in we will use the a-b-c.biopepa model described in section 8.1, from which both state and activity invariants can be infered.

You must select the type of invariants, State or Activity, that you wish to infer from the model (see Figure 49). Following that, you must select the reactions you wish to be included in the analysis (see Figure 50). The results of the analysis for the a-b-c.biopepa model can be seen in Figure 51.

$\includegraphics[scale=0.5]{screenshots/screenshots/infer_invariants1}$

Figure 66: Infering State and Activity Invariants for the model

$\includegraphics[scale=0.5]{screenshots/screenshots/infer_invariants2}$

Figure 67: Choosing reactions to be included in the analysis

$\includegraphics[scale=0.5]{screenshots/screenshots/infer_invariants4}$

Figure 68: Results of the invariants inference for the a-b-c.biopepa model