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

Lookup NU author(s): Professor Anil Wipat

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Abstract

Copyright © 2018 American Chemical Society. 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.

Publication metadata

Author(s): Waites W, Mlslrll G, Cavaliere M, Danos V, Wipat A

Publication type: Article

Publication status: Published

Journal: ACS Synthetic Biology

Year: 2018

Volume: 7

Issue: 12

Pages: 2812-2823

Online publication date: 08/11/2018

Acceptance date: 02/04/2016

ISSN (electronic): 2161-5063

Publisher: American Chemical Society

URL: https://doi.org/10.1021/acssynbio.8b00201

DOI: 10.1021/acssynbio.8b00201

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