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

Author

Listed:
  • Joan Hérisson

    (Université Paris-Saclay)

  • Thomas Duigou

    (Micalis Institute)

  • Melchior Lac

    (Micalis Institute
    Amyris Inc)

  • 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
    Universitat Politècnica de València)

  • Neil Swainston

    (The University of Manchester
    Molecular and Integrative Biology University of Liverpool)

  • 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
    Micalis Institute
    The University of Manchester)

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.

Suggested Citation

  • 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, 2022. "The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32661-x
    DOI: 10.1038/s41467-022-32661-x
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