Single-step versus multi-step optimization. A) An example of an acceptable parameter set describing the wild-type phenotype, which was not successfully optimized by single-step optimization to describe the LXR activated phenotype. This problem was circumvented by multi-step optimization. In the latter case, the parameter estimation is carried out in a step-wise fashion. Hereto, the experimental data is interpolated from the wild-type phenotype to the LXR activated phenotype. At each interpolation step the parameters are reoptimized in order to describe the newly interpolated data. This procedure is repeated until the final state representing phenotype B is reached. B, C) Two examples of corresponding parameter trajectories from the wild-type phenotype to the LXR activated phenotype, normalized by the initial parameters of the wild-type phenotype.