We sincerely apologize for any omissions of relevant work owing to space and reference limitations. D.M.D. acknowledges support from the Office of Naval Research, the Defense Advanced Research Projects Agency, the National Science Foundation, Boston University, and Agilent Technologies. The authors would also like to acknowledge many conversations with colleagues at UC Berkeley, MIT, Harvard, Boston University, BBN Technologies, Autodesk, Agilent, Life Technologies, TeselaGen Biotechnologies, Desktop Genetics, Ginkgo Bioworks, and Genome Compiler. The authors hold financial interests in Lattice Automation Inc., a company developing bio-design automation solutions.