Computer simulations can facilitate the building of models of natural phenomena in research, such as in the molecular life sciences. In order to introduce molecular life science students to the use of computer simulations for model building, a digital case was developed in which students build a model of a pattern formation process in developmental biology using experimental data and computer simulations. For the development of a pedagogical approach, several design principles were used with respect to a suitable model-building method and with respect to increasing the students' understanding of (biological) systems. The case was then developed using this approach. Additional software components have been developed to provide sufficient feedback and support for students who work with the simulations. The case has been evaluated in three 3rd-year undergraduate courses at Wageningen University in the Netherlands and at the University of Zurich in Switzerland. Students appreciated working with the case and answered most exam questions about the contents of the case relatively well. (Contains 5 figures and 3 tables.)