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A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference

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https://pubs.acs.org/doi/abs/10.1021/acssynbio.8b00201
Original languageEnglish
Pages (from-to)2812-2823
Number of pages12
JournalACS Synthetic Biology
Volume7
Issue number12
Early online date8 Nov 2018
DOIs
StatePublished - 2018

Abstract

A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer simulation in any of several languages or robotically assembled in vitro. In this paper we present a language, the Genetic Circuit Description Language (GCDL) and a compiler, the Genetic Circuit Compiler (GCC). This language describes genetic circuits at a level of granularity appropriate both for automated assembly in the laboratory and deriving simulation code. The GCDL follows Semantic Web practice and the compiler makes novel use of the logical inference facilities that are therefore available. We present the GCDL and compiler structure as a study of a tool for generating κ-language simulations from semantic descriptions of genetic circuits.

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