Waites William, Mısırlı Göksel, Cavaliere Matteo, Danos Vincent, Wipat Anil
School of Informatics , University of Edinburgh , Edinburgh EH8 9YL , U.K.
School of Computing and Mathematics , Keele University , Newcastle ST5 5BG , U.K.
ACS Synth Biol. 2018 Dec 21;7(12):2812-2823. doi: 10.1021/acssynbio.8b00201. Epub 2018 Nov 20.
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.
合成生物学的一个核心策略是通过使用相同的构建模块对生物体进行工程改造来理解生物的基本过程。用部件描述的生物机器可以用几种语言中的任何一种通过计算机模拟进行研究，或者在体外进行机器人组装。在本文中，我们展示了一种语言，即遗传电路描述语言（GCDL）和一个编译器，即遗传电路编译器（GCC）。这种语言在适合实验室自动组装和推导模拟代码的粒度级别上描述遗传电路。GCDL遵循语义网实践，并且编译器创新性地利用了由此可用的逻辑推理工具。我们将GCDL和编译器结构作为一种从遗传电路的语义描述生成κ语言模拟的工具的研究来呈现。
