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Virtual Breeding Environments (VBEs) are long-term strategic alliances of organisations aimed at offering the conditions to support the rapid and fluid configuration of Virtual Organisations (VOs). VBE reference models play a guiding role to conceptualise a set of business processes to enhance the responsiveness and flexibility of networks to react to a collaboration opportunity through a collection of collaborative drivers and enablers. VBE reference models serve as a reference guide for the implementation of breeding environments in different domains and application environments. This paper presents an instantiation methodology as a controlled process, addressing systematically a set of steps, supported by different mechanisms and methodologies needed to establish and characterize the management functionalities and running of a VBE that also addresses activities during its entire lifecycle based-on a VBE reference model proposed.