Modeling and simulation in pharmacokinetics has turned into the focus of pharmaceutical companies, driven by the emerging consensus that in silico predictions, combined with in vitro data, have the potential to significantly increase insight into pharmacokinetic processes. To support in silico methodology adequately, software tools need to be user-friendly and, at the same time, flexible. In brief, the software has to allow the modeling of ideas that go beyond the current knowledge--in the form of a virtual laboratory. In this review, we present and discuss the necessary design principles and concepts required to do this. They have been implemented in the software package MEDICI-PK, demonstrating its feasibility and advantages.