Roehner Nicholas, Bartley Bryan, Beal Jacob, McLaughlin James, Pocock Matthew, Zhang Michael, Zundel Zach, Myers Chris J
Raytheon BBN Technologies , Cambridge , Massachusetts 02138 , United States.
Newcastle University , Newcastle upon Tyne NE1 7RU , UK.
ACS Synth Biol. 2019 Jul 19;8(7):1519-1523. doi: 10.1021/acssynbio.9b00092. Epub 2019 Jul 1.
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted extension of the SBOL data standard that allows for the efficient and flexible encoding of combinatorial designs. This extension includes data structures for representing genetic designs with "variable" components that can be implemented by choosing one of many linked designs for existing genetic parts or constructs. We demonstrate the representational power of the SBOL combinatorial design extension through case studies on metabolic pathway design and genetic circuit design, and we report the expansion of the SBOLDesigner software tool to support users in creating and modifying combinatorial designs in SBOL.
随着DNA合成技术和组装方法的改进，使得遗传构建体的组合组装越来越容易实现，用于表示遗传构建体的方法同样需要改进，以应对组合设计空间的指数级增长。为此，我们提出了一种被社区认可的SBOL数据标准扩展，它允许对组合设计进行高效且灵活的编码。此扩展包括用于表示具有“可变”组件的遗传设计的数据结构，这些组件可以通过为现有遗传元件或构建体选择众多链接设计之一来实现。我们通过代谢途径设计和遗传电路设计的案例研究展示了SBOL组合设计扩展的表示能力，并报告了SBOLDesigner软件工具的扩展，以支持用户在SBOL中创建和修改组合设计。
