Electronic design automation (EDA) tools have facilitated the design of ever more complex integrated circuits each year. Synthetic biology would also benefit from the development of genetic design automation (GDA) tools. Existing GDA tools require biologists to design genetic circuits at the molecular level, roughly equivalent to designing electronic circuits at the layout level. Analysis of these circuits is also performed at this very low level. This paper presents the background and issues involved in the development of such a GDA tool for modeling, analysis, and design.

Verification of embedded systems is complicated by the fact that they are composed of digital hardware, analog sensors and actuators, and low level software. In order to verify the interaction of these heterogeneous components, it would be beneficial to have a single modeling formalism that is capable of representing all of these components. To address this need, this paper describes an extended labeled hybrid Petri net (LHPN) model that includes constructs for Boolean, discrete, and continuous variables as well as constructs to model timing. This paper also presents a method to verify these extended LHPNs. Finally, this paper presents a case study to illustrate the application of this model to the verification of a fault-tolerant temperature sensor.

SUMMARY: iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitate the development and maintenance of genetic circuit models as well as both experimental and simulation data records. AVAILABILITY: iBioSim is available for download for Windows, Linux, and MacOS at http://www.async.ece.utah.edu/iBioSim/ CONTACT: [email protected].