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Computational modeling and numerical simulations have become indispensable tools in science, technology, engineering and mathematics (STEM), and in industrial research and development. Consequently, there is growing demand for computational skills in undergraduate and postgraduate students and a need to revise existing curricula. We report from a case study where an existing materials science module was modified to contain numerical simulation of the materials: students use simulation software to explore the material's behavior in simulated experiments. In particular, the Ubermag micromagnetic simulation software package is used by the students in order to solve problems computationally that are linked to current research in the field of magnetism. The simulation software is controlled through Python code in Jupyter notebooks. This setup provides a computational environment in which simulations can be started and analyzed in the same notebook. A key learning activity is a project in which students tackle a given task over a period of approximately 2 months in a small group. Our experience is that the self-paced problem-solving nature of the project work -- combined with the freedom to explore the system's behavior through the simulation -- can facilitate a better in-depth exploration of the course contents. We report feedback from students and educators both on the training in material science and the Jupyter notebook as a computational environment for education. Finally, we discuss which aspects of the Ubermag and the Jupyter notebook have been beneficial for the students' learning experience and which could be transferred to similar teaching activities in other subject areas.