A genetic circuit compiler: generating combinatorial genetic circuits with web semantics and inference
A genetic circuit compiler: generating combinatorial genetic circuits with web semantics and inference
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.
2812-2823
Waites, William
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Mısırlı, Göksel
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Cavaliere, Matteo
60059eb2-b523-4e20-b27e-a9c094c4930d
Danos, Vincent
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Wipat, Anil
3418bbe8-f0f0-4785-8291-cd72fe8b8c3a
21 December 2018
Waites, William
a069e5ff-f440-4b89-ae81-3b58c2ae2afd
Mısırlı, Göksel
870ed782-ecce-4e79-b502-0f775da23c08
Cavaliere, Matteo
60059eb2-b523-4e20-b27e-a9c094c4930d
Danos, Vincent
39d6fea1-0ff9-4f36-8ef7-e81975262c72
Wipat, Anil
3418bbe8-f0f0-4785-8291-cd72fe8b8c3a
Waites, William, Mısırlı, Göksel, Cavaliere, Matteo, Danos, Vincent and Wipat, Anil
(2018)
A genetic circuit compiler: generating combinatorial genetic circuits with web semantics and inference.
ACS Synthetic Biology, 7 (12), .
(doi:10.1021/acssynbio.8b00201).
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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waites-et-al-2018-a-genetic-circuit-compiler-generating-combinatorial-genetic-circuits-with-web-semantics-and-inference
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e-pub ahead of print date: 8 November 2018
Published date: 21 December 2018
Identifiers
Local EPrints ID: 499793
URI: http://eprints.soton.ac.uk/id/eprint/499793
ISSN: 2161-5063
PURE UUID: cc73fe8d-b2eb-4c68-90ff-64b06e9a9efe
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Date deposited: 04 Apr 2025 16:38
Last modified: 22 Aug 2025 02:43
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Contributors
Author:
William Waites
Author:
Göksel Mısırlı
Author:
Matteo Cavaliere
Author:
Vincent Danos
Author:
Anil Wipat
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