Galaxy-SynBioCAD: tools and automated pipelines for Synthetic Biology Design and Metabolic Engineering

Thomas DUIGOU*, Joan HÉRISSON*, Melchior DU 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, Jean-Loup FAULON.
 

There’s a substantial number of tools released around Synthetic Biology and Metabolic Engineering- related questions and needs. This population of tools is difficult to comprehend and use together, main reasons being complexity and interoperability issues. Indeed, a high level of expertise could be required for installing codes, and execution for real life use cases could be computationally resource demanding. Plus some tools, although complementary, use different inputs and outputs which prevent easy chaining. 

The SynBioCAD-Galaxy portal [1] is a growing toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enable 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. 

Tools are made available on GitHub, anaconda.org and the Galaxy Tool Shed, opening to the greatest number access and utilization throughout the SynBio community, and significant effort has been granted for adopting FAIR principles. As a community effort helped by funded projects, the scope covered by tools is expected to expand over time.

The poster will give an overview of the SynBioCAD-Galaxy portal in the context of prediction and construction of E. coli lycopene-producing pathways. The poster will open the discussion around good practices guiding releases of tools through continuous integration. A – lightweight – testing instance of SynBioCAD-Galaxy is available at https://galaxysynbiocad.org.

[1] Hérisson J, Duigou T, du Lac M, Bazi-Kabbaj K, Sabeti Azad M, Buldum G, Telle O, El Moubayed Y, Carbonell P, Swainston N, Zulkower V, Kushwaha M, Baldwin GS, Faulon JL. The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering. Nat Commun., 2022 13(1):5082 | DOI: 10.1038/s41467-022-32661-x | PMID: 36038542

Keywords
Design Automation, Biosynthetic Pathway Engineering, Galaxy workflows, Standards, Web Application