Misirli, G, Wates, W, Cavaliere, M, Danos, V and Wiipat, A (2018) A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference. ACS Synthetic Biology, 7 (12). pp. 2812-2823. ISSN 2161-5063

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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 k-language simulations from semantic descriptions of genetic circuits.

Item Type: Article
Additional Information: The final version of this accepted manuscript can be accessed online at https://pubs.acs.org/doi/10.1021/acssynbio.8b00201
Uncontrolled Keywords: semantic web; inference; program generation; synthetic biology; genetic circuits
Subjects: Q Science > QA Mathematics > QA75 Electronic computers. Computer science
Divisions: Faculty of Natural Sciences > School of Computing and Maths
Depositing User: Symplectic
Date Deposited: 09 Nov 2018 16:51
Last Modified: 18 Jan 2019 12:25
URI: http://eprints.keele.ac.uk/id/eprint/5495

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