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Abstract Summary Rapid development of genomic technologies in recent years enables personalised medicine to become an essential part of healthcare. Advanced computational methods are required to extract relevant insights that can be applied in clinical settings. This presents a challenge for clinicians and biomedical researchers, who need specialised training to adopt these tools. Within the context of PerMedCoE, the first European Centre of Excellence in Personalised Medicine, we developed and delivered a competency-based training programme to support professionals in the life sciences to work with modelling and simulation tools that integrate omics data to identify biological processes relevant to disease. We identified a set of required competencies in the field and built a series of career profiles with specific competence levels in these. The competencies and profiles contributed to define the focus and target audience of the training activities delivered: a combination of self-paced learning resources, webinars and online and face-to-face synchronous courses. The outputs of the programme (competencies, career profiles and training materials) can be used by biomedical professionals for their own career development or to train others. In addition, the approach can be adopted by other fields with rapid technological advancements and a constant need to upskill professionals. Availability and implementation The competency framework is reproduced in full in this paper as supplementary material and available on the Competency Hub at https://competency.ebi.ac.uk/framework/permedcoe/2.1.