Mermaid flowcharts for perturbation design: diagrams-as-code, curated databases, and the E. coli lac operon as a worked example

Planning genetic, pharmacological, or nutritional perturbations is easier when the investigator can state, in advance, which molecular levers are plausible and which readouts would discriminate competing mechanisms. Logic-style flowcharts authored as diagrams-as-code (Mermaid markdown) provide a lightweight, versionable complement to pathway databases, genome browsers, and machine-learning predictors. This methods paper compares three encodings of the E. coli lac operon and recommends layered hybridization of literature logic with RegulonDB-class regulatory facts. Version 1.2 (June 28, 2026): Adds Voigt et al. (2016) synthetic biology framing — GLMP as the inverse of circuit compilation — reference 11, Synthetic biology category tag, updated PDF with embedded figures, and Markdown source file.