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

Methods paper on Mermaid flowcharts for perturbation design, using the E. coli lac operon as a worked example of layered hybridization between literature logic and RegulonDB-class facts. Version 1.3 (June 28, 2026): Replaces raw Mermaid code blocks in the Markdown file with embedded figure PNGs for readable Zenodo preview; retains Voigt et al. (2016) synthetic biology framing from v1.2.

Authors

Institutions

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-06-28
DOI
https://doi.org/10.5281/zenodo.21006264
Primary Topic
Gene Regulatory Network Analysis
Type
preprint
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
preprint

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

Gary Welz
Zenodo (CERN European Organization for Nuclear Research)
Gene Regulatory Network Analysis
preprint

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

Gary Welz
preprint en

Abstract

Methods paper on Mermaid flowcharts for perturbation design, using the E. coli lac operon as a worked example of layered hybridization between literature logic and RegulonDB-class facts. Version 1.3 (June 28, 2026): Replaces raw Mermaid code blocks in the Markdown file with embedded figure PNGs for readable Zenodo preview; retains Voigt et al. (2016) synthetic biology framing from v1.2.

Zenodo (CERN European Organization for Nuclear Research)
The Graduate Center, CUNY (US)
Gene Regulatory Network Analysis
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.

Mermaid flowcharts for perturbation design: diagrams-as-code, curated databases, and the E. coli lac operon as a worked example — Gary Welz · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS