S107: Specification, Design, and Assembly Automation Workflows in Synthetic Biology

Advances in electronic design automation (EDA) have been crucial in the development of complex electronic systems. The ability to independently specify, design, and assemble electronic systems at various abstraction levels has enabled tremendous growth in the semiconductor industry. In addition to growth, EDA has introduced ways to reduce design errors, increase performance, and deliver new products at an increased pace. As the field of synthetic biology grows, it is going to be vital to begin to look at introducing design methodologies that also enable specification, design, and physical assembly. This talk will introduce my vision for creating tools to address these issues which take techniques from EDA and apply them where appropriate to bio-design automation (BDA). In particular I will talk about three efforts, Clotho, Eugene and Cello, which have begun this process. Clotho is a software framework for the retrieval, storage, and manipulation of biological "parts". Eugene is a domain specific language for the specification and constraining of biological "devices".  Cello is a tool for combinational logic synthesis to genetic networks. In addition to discussing these two efforts, I will briefly outline the Center for Integrating Design Automation Research (CIDAR) at Boston University.