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.

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].