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

Joan Hérisson, Thomas Duigou, Melchior Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El Moubayed, Pablo Carbonell, Neil Swainston, Valentin Zulkower, Manish Kushwaha, Geoff S. Baldwin and Jean-Loup Faulon ()
Additional contact information
Joan Hérisson: Université Paris-Saclay
Thomas Duigou: Micalis Institute
Melchior Lac: Micalis Institute
Kenza Bazi-Kabbaj: Micalis Institute
Mahnaz Sabeti Azad: Micalis Institute
Gizem Buldum: Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College
Olivier Telle: Micalis Institute
Yorgo El Moubayed: Micalis Institute
Pablo Carbonell: The University of Manchester
Neil Swainston: The University of Manchester
Valentin Zulkower: University of Edinburgh
Manish Kushwaha: Micalis Institute
Geoff S. Baldwin: Imperial College Centre for Synthetic Biology, Department of Life Sciences, Imperial College
Jean-Loup Faulon: Université Paris-Saclay

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-32661-x

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