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The development of computer-aided design tools for synthetic biology is currently a hot research topic. However the field is not mature enough to provide a generic, adaptable and reliable tool for potential applications. The purpose of this paper is to present a system designers approach. We highlight, through the work carried out by our team in recent years, the potential, but also the difficulties, of structuring an assisted design flow for synthetic biology. For this task, our idea is to build the design flow for synthetic biology on the foundations of the Electronic Design Automation tools that have proven their efficiency during the past 30 years. Although the overall approach of the microelectronics can be adapted to synthetic biology, some specific steps have to be created from scratch.