We develop computational and omic-wide methods to identify and validate new biomarkers for personalised diagnosis and prognosis of diseases. Before these methods can be used in patient care they have to be implemented as regulated software. Regulated software is software that has to conform to some legislation. Legislation requires software development to be conform to IEC/ISO standards. We have a software that is intended to be used as a in-vitro diagnostic. So we had to establish an IEC 62304 conform software development process. Here we share some insights about: our tool stack, our processes, handling a lot of documents and how it all links to software engineering best practices and reproducible science.