The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.
The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.
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DOI：
10.1038/s41467-022-32661-x
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发表时间：
2022-08-29
影响因子：
16.6
通讯作者：
Faulon, Jean-Loup
中科院分区：
文献类型：
--
作者：
Herisson, Joan;Duigou, Thomas;du Lac, Melchior;Bazi-Kabbaj, Kenza;Azad, Mahnaz Sabeti;Buldum, Gizem;Telle, Olivier;El Moubayed, Yorgo;Carbonell, Pablo;Swainston, Neil;Zulkower, Valentin;Kushwaha, Manish;Baldwin, Geoff S.;Faulon, Jean-Loup
在这里，我们介绍Galaxy-SynBioCAD门户网站，一个合成生物学，代谢工程和工业生物技术的工具箱。目前在门户网站上共享的工具和工作流程使人们能够构建产生所需化学靶标的菌株库，涵盖从菌株和靶标的选择、待组装的DNA部分的设计到驱动用于质粒组装和菌株转化的液体处理器的脚本的生成的端到端代谢途径设计和工程化过程。标准格式如SBML和SBOL贯穿始终，以加强工具的兼容性。在四个不同地点进行的一项研究中，我们通过建立一个E.大肠杆菌产溶菌酶菌株。我们还对我们的工作流程进行了文献和专家验证的途径。总体而言，我们发现在工作流程生成的前10个路径中检索验证路径的成功率为83%。自动化设计和构建过程可以快速加速合成生物学和代谢工程的工作。在这里，作者介绍了Galaxy-SynBioCAD，这是一个用于合成生物学，代谢工程和工业生物技术的工具箱，他们用来通过自动生成驱动机器人工作站的脚本来构建和执行从途径设计到应变工程的Galaxy科学工作流程。
Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows. Automated design and build processes can rapidly accelerate work in synthetic biology and metabolic engineering. Here the authors present Galaxy-SynBioCAD, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology that they use to build and execute Galaxy scientific workflows from pathway design to strain engineering through the automated generation of scripts driving robotic workstations.
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影响因子：
14.9
作者：
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通讯作者：
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影响因子：
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影响因子：
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作者：
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通讯作者：
Faulon, Jean-Loup