Transcranial Magnetic Stimulation (TMS) is a new technique for brain stimulation. TMS has several applications in medical and clinical research. Its use, however is still empirical and requires many stimulations to find the best coil position for stimulation. We have developed a simulation software of transcranial magnetic stimulation which computes the electromagnetic field induced in the cortex by TMS. This object-oriented software development has been revisited with a model driven approach. We have organised this article in two main parts. First the simulation tool with the computation of potential magnetic field outside the head is described. Then, we discuss the software engineering problems encountered with some possible solutions. The experience gained in this development is finally sketched in a model for software versioning.