The third step is to solve the variational equation along this solution and to use this to calculate the derivatives of the solution of interest with respect to all the parameters. These steps are needed for all the subsequent analysis. At this stage one already has several classical (e.g. period, phase and amplitude derivatives) and new (e.g. infinitesimal response curves (IRCs) and phase IRCs) analysis tools available. These outputs can be selected using the graphical interface. This process involves significant computation and therefore using the graphical interface one can configure what aspects need to be computed and see how accurate the computation is likely to be. For the latter, after being presented with an informative analysis, the user can opt to re-calculate the fundamental matrices (the building blocks of the analysis, described in more detail in the manual) by increasing the time resolution at which the computations are done. More details about the time resolution required are outlined in the accompanying manual. If the user has a copy of the MATLAB Parallel Computing Toolbox installed, then they will be given the option of running the analysis using one of the user defined parallel configurations. The computation of the fundamental matrices is ideal for parallelisation and a substantial speed-up can be achieved.
The solution derivatives can be used as a predictive tool to show how combined parameter changes will affect the model dynamics (without performing tedious manual changes by hand first) and what sort of experimental data features the model will be able to match under these parameter changes. For a further example of this type predictive analysis, we point the reader to our paper  (c.f. Table 2 and Additional file 1). 2b1af7f3a8