In silico implementation of synthetic gene networks.

Mario Andrea Marchisio

Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland. mario.marchisio@bsse.ethz.ch

Methods in molecular biology (Clifton, N.J.) 2012

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Computational synthetic biology has borrowed methods, concepts, and techniques from systems biology and electrical engineering. Features of tools for the analysis of biochemical networks and the design of electric circuits have been combined to develop new software, where Standard Biological Parts (physically stored at the MIT Registry) have a mathematical description, based on mass action or Hill kinetics, and can be assembled into genetic networks in a visual, "drag & drop" fashion. Recent tools provide the user with databases, simulation environments, formal languages, and even algorithms for circuit automatic design to refine and speed up gene network construction. Moreover, advances in automation of DNA assembly indicate that synthetic biology software soon will drive the wet-lab implementation of DNA sequences.