Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Washington St MC 0477, Blacksburg VA 24061, USA.
Nucleic Acids Res. 2010 May;38(8):2637-44. doi: 10.1093/nar/gkq086. Epub 2010 Feb 18.
One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard have prompted the development of multiple new standards proposing different avenues to overcome these shortcomings. The lack of compatibility between standards, the compliance of parts with only some of the standards or even the type of constructs that each standard supports have significantly increased the complexity of assembling constructs from standardized parts. Here, we describe computer tools to facilitate the rigorous description of part compositions in the context of a rapidly changing landscape of physical construction methods and standards. A context-free grammar has been developed to model the structure of constructs compliant with six popular assembly standards. Its implementation in GenoCAD makes it possible for users to quickly assemble from a rich library of genetic parts, constructs compliant with any of six existing standards.
合成生物学的基础之一是开发标准化遗传部件库的项目，这些部件可以快速、廉价地组装成大型系统。最初的 BioBrick 标准的局限性促使开发了多个新的标准，提出了不同的方法来克服这些缺点。标准之间缺乏兼容性、部件仅符合部分标准甚至每个标准支持的构建类型，这些都大大增加了从标准化部件组装构建体的复杂性。在这里，我们描述了计算机工具，以方便在快速变化的物理构建方法和标准的背景下，对部件组成进行严格描述。已经开发了一种上下文无关语法来模拟符合六种流行组装标准的构建体的结构。它在 GenoCAD 中的实现使用户能够快速地从遗传部件库中组装，这些部件符合六种现有标准中的任何一种。
