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Scientific workflows have recently emerged as a new paradigm for scientists to formalize and structure complex and distributed scientific processes to enable and accelerate many scientific discoveries. In contrast to business workflows, which are typically control flow oriented, scientific workflows tend to be dataflow oriented, introducing a new set of requirements for system development. These requirements demand a new architectural design for scientific workflow management systems (SWFMSs). Although several SWFMSs have been developed that provide much experience for future research and development, a study from an architectural perspective is still missing. The main contributions of this paper are: (i) based on a comprehensive survey of the literature and identification of key requirements for SWFMSs, we propose the first reference architecture for SWFMSs, (ii) in compliance with the reference architecture, we further propose a service-oriented architecture for VIEW (a VIsual sciEntificWorkflow management system), (iii) we implement VIEW to validate the feasibility of the proposed architectures, and (iv) we present two case studies to showcase the applications of our VIEW system.