A Rule-Based Design Specification Language for Synthetic Biology
A Rule-Based Design Specification Language for Synthetic Biology
复制标题
合成生物学基于规则的设计规范语言
DOI：
10.1145/2641571
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
D. Densmore
中科院分区：
文献类型：
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作者：
Ernst Oberortner;Swapnil P Bhatia;Erik Lindgren;D. Densmore
合成生物学是一门工程学科，其中部分 DNA 序列被组合成新颖、复杂的系统，以执行所需的生物学功能。功能良好且表现良好的生物系统遵循一套特定的生物“规则”。数据交换标准和生物设计自动化 (BDA) 工具支持零件库的组织和符合规则的组合物的探索。在这项工作中，我们正式定义了一种设计规范语言，使生物规则能够集成到合成生物学工程过程中。支持的规则分为五类：计数、配对、定位、方向和交互。我们正式定义每个规则的语义，描述语言的表达能力，并进行案例研究，我们按照两种替代范式（基于规则和模板驱动）迭代设计遗传优先编码器电路。最终，我们采用了一种方法来近似计算枚举所有符合规则的设计的复杂性和时间。我们的规范语言可能或可能不足以表达合成生物学家可能想要描述的所有设计，或者通过实验可能发现的复杂性。然而，为了理解生物学的功能，对生物学规则的获取、规范、管理和应用的计算支持是不可避免的。
Synthetic Biology is an engineering discipline where parts of DNA sequences are composed into novel, complex systems that execute a desired biological function. Functioning and well-behaving biological systems adhere to a certain set of biological “rules”. Data exchange standards and Bio-Design Automation (BDA) tools support the organization of part libraries and the exploration of rule-compliant compositions. In this work, we formally define a design specification language, enabling the integration of biological rules into the Synthetic Biology engineering process. The supported rules are divided into five categories: Counting, Pairing, Positioning, Orientation, and Interactions. We formally define the semantics of each rule, characterize the language's expressive power, and perform a case study in that we iteratively design a genetic Priority Encoder circuit following two alternative paradigms—rule-based and template-driven. Ultimately, we touch a method to approximate the complexity and time to computationally enumerate all rule-compliant designs. Our specification language may or may not be expressive enough to capture all designs that a Synthetic Biologist might want to describe, or the complexity one might find through experiments. However, computational support for the acquisition, specification, management, and application of biological rules is inevitable to understand the functioning of biology.