title: Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.
abstract: BACKGROUND
  The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry.
  
  
  RESULTS
  To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks.
  
  
  CONCLUSIONS
  Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.
authors.affiliation: BBN Technologies, Cambridge, Massachusetts, United States of America. jakebeal@bbn.com
authors.forename: Jacob
authors.initials: J
authors.lastname: Beal
authors.forename: Ting
authors.initials: T
authors.lastname: Lu
authors.forename: Ron
authors.initials: R
authors.lastname: Weiss
mesh_terms: D004247:DNA / Q000737:chemistry / Q000235:genetics; D053263:Gene Regulatory Networks / Q000235:genetics*; D011381:Programming Languages; D058615:Synthetic Biology
chemical_list: D004247:DNA