Building models to describe processes forms an essential part of molecular biology research. However, in molecular biology curricula little attention is generally being paid to the development of this skill. In order to provide students the opportunity to improve their model building skills, we decided to develop a number of digital cases about developmental biology. In these cases the students are guided to build a model according to a method that is based on expert analysis and historical data; they first build a simplified model based on the wild-type only and then they extend this model step by step based on experimental results. After each extension, the biological implications of the extension are evaluated. The first case was evaluated three times during a regular course at Wageningen University, The Netherlands and once at the University of Zurich, Switzerland. The analysis of audio tapes revealed that students did indeed engage in the reasoning processes, which are typical for model building. Furthermore, exam results seem to suggest that working with the case indeed facilitates model building in analogical situations and the students judged working with the case positively.