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Journal Articles Nature Communications Year : 2022

The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering

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Valentin Zulkower

Abstract

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.
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Dates and versions

hal-03649340 , version 1 (22-04-2022)
hal-03649340 , version 2 (30-08-2022)

Identifiers

Cite

Joan Hérisson, Thomas Duigou, Melchior Du Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, et al.. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nature Communications, 2022, ⟨10.1038/s41467-022-32661-x⟩. ⟨hal-03649340v2⟩
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