Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.
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DOI：
10.1371/journal.pone.0018882
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发表时间：
2011-04-29
期刊：
影响因子：
3.7
通讯作者：
Densmore D
中科院分区：
文献类型：
--
作者：
Bilitchenko L;Liu A;Cheung S;Weeding E;Xia B;Leguia M;Anderson JC;Densmore D
合成生物系统目前是通过特殊的、迭代的规范、设计和组装过程创建的。这些系统将极大地受益于对所需系统组件的更正式和更严格的规范以及对其组成的限制。因此，创建强大而高效的设计流程和工具势在必行。我们提出了一种人类可读的语言(尤金)，它允许基于生物部件的合成生物设计的规范，并提供了一个非常有表现力的约束系统来驱动从单个部件的集合自动创建组合部件(设备)。我们在三个不同的领域展示了尤金的能力：设备规范、设计空间探索以及装配和仿真集成。这些结果突出了尤金创造组合设计空间并修剪这些空间用于模拟或物理组装的能力。尤金快速、经济高效地创建了功能设计。Eugene用于基于DNA的设备的正向工程，并通过其数据类型和执行语义反映了合成生物学中所需的抽象层次。Eugene提供了一个强大的约束系统，可用于在运行时驱动新设备的创建。它是一个更大的工具链的一部分，包括对设计、模拟和物理设备组装的支持，从而实现了所有这些。
Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.
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