Towards programming languages for genetic engineering of living cells
Towards programming languages for genetic engineering of living cells
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DOI：
10.1098/rsif.2008.0516.focus
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发表时间：
2009-08-06
影响因子：
3.9
通讯作者：
Phillips, Andrew
中科院分区：
文献类型：
--
作者：
Pedersen, Michael;Phillips, Andrew
合成生物学旨在生产新颖的生物系统来执行一些理想的和定义明确的功能。一个最终的梦想是使用基于工程的工具和编程语言在高级抽象中设计这些系统，按下按钮，并将设计转换为可以合成的DNA序列，这些序列可以合成并在活细胞中工作。我们介绍了这样的编程语言，该语言允许以模块化方式表达潜在未确定的蛋白质和基因之间的逻辑相互作用。编译器可以将程序翻译成标准生物学部分的序列，该过程依赖于逻辑编程和包含已知生物学部分和蛋白质相互作用的原型数据库。程序也可以转化为反应，从而可以进行模拟。尽管目前对可用数据的限制阻止了在实际应用中充分利用该语言，但该语言可用于开发合成系统的正式模型，否则这些模型通常由非正式符号表示。该语言还可以作为一个具体的建议，可以讨论未来的语言设计，并可以帮助指导迄今为止侧重于生物学的零件特性而不是逻辑性的生物学部分的新兴标准。
Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesized and put to work in living cells. We introduce such a programming language, which allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner. Programs can be translated by a compiler into sequences of standard biological parts, a process that relies on logic programming and prototype databases that contain known biological parts and protein interactions. Programs can also be translated to reactions, allowing simulations to be carried out. While current limitations on available data prevent full use of the language in practical applications, the language can be used to develop formal models of synthetic systems, which are otherwise often presented by informal notations. The language can also serve as a concrete proposal on which future language designs can be discussed, and can help to guide the emerging standard of biological parts which so far has focused on biological, rather than logical, properties of parts.