Our aim is to reconstruct Claude Bernard’s empirical investigations with a computational model. We suppose that Bernard had in mind what we call core models that contain the basic physiological concepts upon which Bernard builds his general physiological theory. The core models provide a simplified view of physiology, which allows Bernard to make hypotheses and to draw out their logical consequences. We show how those core models are specified using both description logics and multi-agent systems. Then, we explain how it is possible to build, on these core models, a virtual experiment laboratory, which lets us construct and conduct virtual experiments that play a role similar to that of thought experiments. More generally, we attempt to correlate Bernard’s experiments, performed to corroborate or refute some of his working hypotheses, to virtual experiments emulated on core models.