Genetic design automation

Researchers are now able to engineer synthetic genetic circuits for a range of applications in the environmental, medical, and energy domains. Crucial to the success of these efforts is the development of methods and tools for genetic design automation (GDA). While inspiration can be drawn from experiences with electronic design automation (EDA), design with a genetic material poses several challenges. In particular, genetic circuits are composed of very noisy components making their behavior more asynchronous, analog, and stochastic in nature. This talk presents our research in the development of the GDA tool, iBioSim, which leverages our past experiences in asynchronous circuit synthesis and formal verification to address these challenges. The iBioSim tool enables the synthetic biologist to construct models in a familiar graphical form, analyze them using a variety of methods that leverage efficient abstractions, visualize their analysis results using an intuitive interface, and ultimately synthesize a genetic implementation from a library of genetic parts. Each step of this design process utilizes standard data representation formats enabling the ready exchange of results.