Biologists and engineers are working together to develop the field of synthetic biology. These researchers are attempting to design synthetic genetic circuits that enable bacteria to consume toxic waste, destroy tumors, and produce drugs and bio-fuels. While experimental methods for genetic engineering have existed for a long time, synthetic biology adds a principled design methodology that is supported by repositories of standard parts, high-level model abstractions, and an automated construction process. Since these are the cornerstones of electronic design automation (EDA) which has enabled the design of more complex computer chips each year, it is logical that experiences with EDA will be leveraged during the development of genetic design automation (GDA).
Intellectual merit: This project will develop a comprehensive and integrated suite of GDA tools to support efficient analysis and design of synthetic genetic circuits. These tools will leverage and extend standards, such as the Systems Biology Markup Language (SBML) and Synthetic Biology Open Language (SBOL), to allow for the exchange of models and designs with other researchers. Our research will develop new modeling, analysis, and visualization methods that enable the study of the dynamic behavior of bacterial populations. The efficiency of these tools will be enhanced using automated model abstraction and parallel computer algorithms. PI's design tools will exploit techniques developed for asynchronous (clock-less) integrated circuits. PI will work with experimental collaborators to validate the research results.
Broader Impacts: Due to the wide applications being proposed for synthetic biology ranging from drug production and gene therapies to biofuels, the potential impact of this research is significant. This research will bring together people in theory and modeling with those doing experimental work. This project will also support the development of extensions to standards enabling the development of ever more complex systems. These standards as well as all software developed in this project will be released into the public domain. The PI is committed to the integration of research with education through the development of course materials and working with undergraduates.
