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All IMDEA institutes have a similar organisational structure and function. They are non-profit making organisations (public foundations) in which their sponsors and scientific advisers play a crucial role.

The Scientific Advisory Board are made up of researchers of acknowledged international experience in each IMDEA’s area of expertise and are independent from the institutes themselves. Committee roles include supervising and advising the Director of the Institute in the development of scientific programmes and recruitment of staff as well as overseeing technical and scientific evaluations of activities carried out and results obtained.