CAREER: Design Automation Infrastructure for DNA Assembly in Synthetic Biology

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Intellectual MeritSynthetic biology attempts to design novel biological systems to address a number of challenges in bioenergy, biotherapeutics, and bioremediation. Synthetic biology computational tools must be closely coupled to experimental needs to transform the field. A critical opportunity for this coupling is the DNA assembly process. This project addresses the challenge of physically assembling DNA in an automated, optimized and efficient software and liquid handling workflow for a number of applications and assembly chemistries. This project will: (1) Develop a software library for DNA assembly protocols; (2) develop application software to create and manipulate DNA protocol and assembly graphs; (3) develop a common instruction set to abstract low level liquid handling; (4) experimentally create large, complex genetic regulatory networks (GRNs); and (5) expand synthetic biology outreach to K-12, undergraduate, graduate, and postdoctoral students to include automated DNA assembly. Broader ImpactsMaking open source, freely available DNA assembly software widely employed will change the entire "design-build-test" cycle proposed by synthetic biology. Industrially supported liquid handling robotic operations will unify the domain and make the creation of novel living systems cheaper, more reliable, and more accessible. The project's software will be the first of its kind publicly available. Educational outreach will be continued to introduce synthetic biology to underrepresented groups, undergraduates, and high school students thus training a future generation of engineering students. DNA assembly education will be made available to the International Genetically Engineered Machine (iGEM) software division. A "Registry of Synthetic Biology Software Tools" will be expanded to provide a community resource for bio-design automation software. Finally, the International Workshop on Bio-Design Automation (IWBDA) will expand its educational mission to provide additional DNA assembly tutorials, a PhD forum, and a formal mentorship program to match students with academic and industrial mentors.