Galaxy-SynBioCAD

Galaxy-SynBioCAD enables design and engineering of metabolic pathways to generate microbial strain libraries for production of target chemicals.

Key Features:

• End-to-End Workflow Support: Provides a workflow from strain and target selection through DNA part assembly and script generation for automation in plasmid construction and strain transformation.
• Standardized Data Formats: Uses SBML (Systems Biology Markup Language) and SBOL (Synthetic Biology Open Language) to ensure interoperability and data exchange.
• Practical Application and Validation: Was applied across four distinct sites to develop a library of Escherichia coli strains capable of producing lycopene.
• Benchmarking and Success Rates: Workflows were benchmarked against literature-validated pathways and retrieved validated pathways at an 83% success rate among the top ten generated.

Scientific Applications:

• Synthetic Biology: Supports pathway design and genetic part assembly for synthetic biology projects.
• Metabolic Engineering: Enables engineering of metabolic pathways for production of target chemicals.
• Industrial Biotechnology: Facilitates development of microbial strains for industrial-scale biochemical production.
• Strain Library Generation: Enables construction of libraries of engineered microbial strains for targeted compound biosynthesis, exemplified by lycopene in Escherichia coli.

Methodology:

Computational steps explicitly include strain and target selection, DNA part assembly, script generation for automation in plasmid construction and strain transformation, use of SBML and SBOL standardized formats, and generation and ranking of pathways with benchmarking against literature-validated pathways (retrieval of validated pathways among the top ten).