Interdisciplinary Computing and Complex Biosystems, School of Computing, Newcastle University, Newcastle upon Tyne, UK.
Department of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, CO, USA.
Methods Mol Biol. 2025;2850:89-104. doi: 10.1007/978-1-0716-4220-7_6.
Synthetic biology, also known as engineering biology, is an interdisciplinary field that applies engineering principles to biological systems. One way to engineer biological systems is by modifying their DNA. A common workflow involves creating new DNA parts through synthesis and then using them in combination with other parts through assembly. Assembly standards such as MoClo, Phytobricks, and Loop are based on Golden Gate, and provide a framework for combining parts. The Synthetic Biology Open Language (SBOL) has implemented a best practice for representing build plans to communicate them to other practitioners through whiteboard designs and in a machine-readable format for communication with lab automation tools. Here we present a software tool for creating SBOL representations of build plans to simulate type IIS-mediated assembly reactions and store relevant metadata.
合成生物学，也被称为工程生物学，是一门应用工程学原理于生物系统的跨学科领域。一种对生物系统进行工程设计的方法是对其 DNA 进行修饰。一种常见的工作流程是通过合成创建新的 DNA 片段，然后通过组装将它们与其他部分组合在一起。MoClo、Phytobricks 和 Loop 等组装标准基于 Golden Gate，并为组合部件提供了一个框架。合成生物学开放语言 (SBOL) 实施了一种最佳实践，用于表示构建计划，以便通过白板设计和机器可读格式将其传达给其他从业者，并与实验室自动化工具进行通信。在这里，我们提出了一个用于创建 SBOL 表示构建计划的软件工具，以模拟 Type IIS 介导的组装反应并存储相关元数据。
