A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.,ACS Synthetic Biology

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A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.
ACS Synthetic Biology ( IF 3.7 ) Pub Date : 2018-11-20 , DOI: 10.1021/acssynbio.8b00201
William Waites ₁ , Göksel Mısırlı ₂ , Matteo Cavaliere ₃ , Vincent Danos _{1,

4} , Anil Wipat ₅

Affiliation

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.

中文翻译：

遗传电路编译器：使用Web语义和推理生成组合遗传电路。

合成生物学的中心策略是通过工程生物使用相同的构件来了解生物的基本过程。可以用几种语言中的任何一种通过计算机模拟来研究以零件描述的生物机器，或者可以在体外自动组装。在本文中，我们介绍了一种语言，即遗传电路描述语言（GCDL）和一种编译器，即遗传电路编译器（GCC）。该语言以适合于实验室中自动组装和派生模拟代码的粒度级别描述遗传电路。GCDL遵循语义Web惯例，并且编译器新颖地利用了因此可用的逻辑推理功能。

更新日期：2018-11-08

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