Genetic Design (BASIC Assembly)

• This workflow encodes the top-ranking predicted pathways from the previous workflow into plasmids intended to be expressed in the specified organism. BASIC is used as assembly method.
• It provides ECHO® liquid handler instructions file.
• pub DOI: 10.1016/j.isci.2025.113599

input:

• Sampling file: csv file : The CSV file should contain cell-free components combination. This data will be passed to the icFree_extractor & icFree_learner tools.

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This workflow encodes the top-ranking predicted pathways from the previous workflow into plasmids intended to be expressed in the specified organism. Assembly methods are Gibson, Golden or Ligation Chain Reaction.

Annotation: Evaluating and ranking a set of pathways based on multiple metrics. Given a set of pathways generated by RetroPath2.0, this workflow informs the user as to the theoretically best performing ones based on the four criteria (target product flux, thermodynamic feasibility, pathway length, and enzyme availability).

Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools