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.21006464

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

The paper aims to introduce Mermaid flowcharts as a tool for designing perturbations in synthetic biology.
Describes the use of Mermaid flowcharts for visual explanations of design processes.
Includes a worked example focusing on the E. coli lac operon.
Presents two file formats: PDF and Markdown with embedded figures.
Provides a practical framework for creating diagrams-as-code in perturbation design.
Highlights the advantages of curated databases for synthetic biology applications.

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Implication

Methods paper demonstrates using Mermaid flowcharts for perturbation design, outlining a practical example for E. coli.

Abstract

Methods paper on Mermaid flowcharts for perturbation design, E. coli lac operon worked example. Version 1.5: two self-contained files only (PDF + Markdown with embedded figures). Voigt et al. (2016) synthetic biology framing included.

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Gary Welz (2026) studied this question.

synapsesocial.com/papers/6a435cb3759b888809a5309a https://doi.org/10.5281/zenodo.21006464

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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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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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Implication

Abstract

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