8.4 Comparing with external data

As part of the Bio-PEPA Eclipse Plug-in experimentation feature, you can also import external data from a .csv file, or a Systems Biology Software Infrastructure (SBSI) format file (for more information on SBSI see [7]), i.e. an .sbsidata file and plot them along with the results of the Bio-PEPA analysis you are performing (see Figure 38).

\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare1}
Figure 56: You can import data from external sources to compare against model results


Importing data from a .csv file

In order to take advantage of this feature, you have to set a comma-separated values (.csv) file to import data from, as shown in Figure 39. As an example, here we are performing a simulation run of the a-b-c.biopepa model and importing data from a previous experiment on the same model, which we have stored in a-b-c_results.csv. Figure 40 shows the chosen .csv file, as it appears in the dialogue box. You may choose a different .csv file by clicking on the Change button. Clicking on the Finish button produses the resulting graphs from the simulation and the imported data. In our case the two graphs are shown in Figure 41.

\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare2}
Figure 57: Choosing a .csv file to import data from
\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare3}
Figure 58: An external .csv file has been set
\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare4}
Figure 59: The resulting graph for the simulation of the a-b-c.biopepa model, in comparison to the plotted imported data from the a-b-c_results.csv file


Importing data from a SBSI format file

You have to set a Systems Biology Software Infrastructure (SBSI) format file (for more information on SBSI see [7]), i.e. a .sbsidata file to import data from, as shown in Figure 42. Figure 43 shows the chosen ABC_10000_reduced1.sbsidata file, as it appears in the dialogue box. You may choose a different .sbsidata file by clicking on the Change button. Clicking on the Finish button produses the resulting graphs from the simulation and the imported data. In our case the two graphs are shown in Figure 44.

\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare6}
Figure 60: Choosing a .sbsidata file to import data from
\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare7}
Figure 61: An external .sbsidata file has been set
\includegraphics[scale=0.5]{screenshots/screenshots/experimentcompare8}
Figure 62: The resulting graph for the simulation of the a-b-c.biopepa model, in comparison to the plotted imported data from the ABC_10000_reduced1.sbsidata file