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.21006439

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 explore the application of Mermaid flowcharts in perturbation design, highlighting its utility through the E. coli lac operon.
Presented a methods framework for using Mermaid flowcharts in perturbation design.
Utilized the E. coli lac operon as a worked example to illustrate the approach.
Incorporated synthetic biology principles from Voigt et al. (2016).
Provided a structured guide to creating perturbation designs using Mermaid flowcharts.
Demonstrated effective integration of diagrams-as-code within synthetic biology contexts.

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Implication

Methods paper demonstrates perturbation design using Mermaid flowcharts in synthetic biology, indicating a practical approach for researchers.

Abstract

Methods paper on Mermaid flowcharts for perturbation design, using the E. coli lac operon as a worked example. Version 1.4 (June 28, 2026): Figures embedded inside the PDF and Markdown (self-contained); Voigt et al. (2016) synthetic biology framing included.

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Gary Welz (2026) studied this question.

synapsesocial.com/papers/6a435c8c759b888809a52f73 https://doi.org/10.5281/zenodo.21006439

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

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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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Abstract

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