Factories of the future must be capable to adapt themselves to continuously changing market demand. Therefore new manufacturing technologies are needed: from agile operating machines up to internet based services. In particular, new advanced automation solutions, that integrate all factory levels in a unique real time framework, are mandatory. Nowadays, neither accepted standards nor assessed development methodologies and software environments are available to support industries when facing such a crucial issue. In the present contribution an open and modular automation system architecture is proposed, based on emerging modelling paradigms and recent international standards. Furthermore, a methodology to develop self-adaptive factory automation solutions is illustrated, using a novel modular simulation based method to verify digitally -through a modular bottom up approach -the correctness of real size automation systems. The proposed framework has been applied to a highly innovative reconfigurable factory for personalised shoes production. Such a real-size industrial application proves the effectiveness and the benefits of the presented methods for the development of complex automation solutions for high value added production systems.