The Bio-PEPA Eclipse Plug-inUser Manual: Creating experiments

8.2 Creating experiments

As part of the time-series analysis, the Bio-PEPA Eclipse Plug-in allows you to create and save experiments, which you can re-run later. The user may choose to have the results of the experiments plotted on the same or separate graphs, or for them to be stored in a comma-separated values (.csv) file (see Figure 26).

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Figure 45: Bio-PEPA allows you to create and save experiments which you can re-run later

Disabling one or more reactions

One of the options offered by the experimentation feature of the Bio-PEPA Eclipse Plug-in allows the user to disable one or more of the reactions of the model. For example, in Figure 27 the user has chosen to disable the reaction $\mathit{a1}$ of the a-b-c.biopepa model described in section 8.1. The results of the experiment are shown in Figure 28.

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Figure 46: Disabling reaction $a1$ of the a-b-c.biopepa model

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Figure 47: The resulting graphs when the $\mathit{a1}$ reaction has been disabled and when it is on

Altering the initial populations

Additionally, the user may alter the initial populations of the species of the Bio-PEPA model by providing, either a set of comma-separated values, or a range of values. In Figure 29, the user has provided two comma-separated values for the initial population of species $A$ of the a-b-c.biopepa model, 40 and 50. The resulting graphs for this experiment are shown in Figure 30.

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Figure 48: Setting comma-separated values for species $A$ of the a-b-c.biopepa model

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Figure 49: The resulting graphs of a stochastic simulation for the two different initial populations of species $A$

Varying the rate values

Finally, the user may alter the values of the rate (kinetic) variables of the model by providing, either a set of comma-separated values, or a range of values. In Figure 31, the user has provided a range of values for kinetic parameter $r1$ of the a-b-c.biopepa model, by setting a start value of 0.0050, a stop value of 0.01 and a step of 0.0050. The resulting graphs for this experiment are shown in Figure 32.

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Figure 50: Setting a range of values for kinetic parameter $r1$ of the a-b-c.biopepa model

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Figure 51: The resulting graphs for the two different values of the $r1$ kinetic parameter