Synthetic biology is an emerging field at the interface between biotechnology and engineering sciences. It aims at designing new biological functions by assembling elementary parts (DNA sequences) based on design approaches inspired from those used for the design of complex microsystems. The development of efficient tools to support the design is therefore a technological bottleneck that could prevent the development of this technology. This issue is tackled in this paper by reusing as much as possible the existing design flow of heterogeneous microsystems. Focus is put on modeling and simulation tasks for which biology differs from standard physical domains by different aspects. In this paper, some methods that have been implemented to address these issues are discussed. The main shortcoming is that they lead to models that are far more complex than their electronics counterparts. As a consequence, simulation time becomes a big challenge in design processes. A solution suggested in the last section consists in simulating these models on Graphics Processing Unit, with a x40 speed up.