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

Gary Welz

doi:10.5281/zenodo.21006713

June 28, 2026Open Access

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

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Key Points

This paper aims to introduce Mermaid flowcharts as a method for designing biological perturbations, exemplified by the E. coli lac operon.
Utilized Mermaid flowcharts for visual representation of perturbation designs.
Employed the E. coli lac operon as a specific case study.
Provided clarity through PDF documentation and source availability on GitHub.
Illustrated the effectiveness of Mermaid flowcharts for simplifying perturbation design.
Demonstrated the integration of curated databases for improved functionality.
Highlighted applications in synthetic biology through the chosen example.

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Implication

Methods paper demonstrates how to use Mermaid flowcharts to design perturbations in E. coli, suggesting clarity in biological modeling.

Abstract

Methods paper on Mermaid flowcharts for perturbation design, using the E. coli lac operon as a worked example. Primary document: PDF (figures embedded). Version 1.6 (June 28, 2026): PDF-only deposit for clarity; Markdown source remains on GitHub. Includes Voigt et al. (2016) synthetic biology framing (reference 11).

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Gary Welz (2026) studied this question.

synapsesocial.com/papers/6a435cb3759b888809a530a3 https://doi.org/10.5281/zenodo.21006713

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

Key Points

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

Key Points

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