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Systems Medicine has emerged as an integrated approach to biomedical research and personalised healthcare allowing for the development of new strategies for individualised diagnosis, treatment and prevention of diseases. To achieve these ambitious goals we need to bridge the gap between experimental data and medical knowledge as well as evaluate both in terms of clinical utility and patient’s benefit. Towards this purpose, the European Association of Systems Medicine (EASyM) is organising the second International Conference on Systems Medicine entitled “Big Data: transition to practice”, which will give delegates a flavour of cutting edge research and translation of it to the clinics within the field. The conference is designed to initiate and promote interactions between researchers and clinicians who are interested in applying systems level approaches to address medical problems.