Cellular processes are governed by complex networks of interacting genes and proteins. Theoretical molecular biologists attempt to describe these processes via mathematical models by writing biochemical reaction equations. Modellers are building increasingly larger and complex mathematical models to describe these cellular processes, making model evaluation a time consuming and difficult task. The authors describe an automatable process for model evaluation and a software system that implements this process. The software is adaptable to many types of models and is freely available along with all needed data files. The cell cycle control system for budding yeast is known in fine detail and constrained by more than 100 phenotypic observations in mutant strains. As an example, the authors apply their process to a model of cell cycle control in budding yeast containing dozens of regulatory equations and explaining nearly all of the known mutant phenotypes.