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Markdown Mermaid Writing

  • 985 installs
  • 32k repo stars
  • Updated July 29, 2026
  • k-dense-ai/scientific-agent-skills

markdown-mermaid-writing is a documentation skill that generates publication-ready scientific and technical markdown reports with accurate embedded Mermaid diagrams for developers and researchers documenting experiments

About

markdown-mermaid-writing is a skill from k-dense-ai/scientific-agent-skills that produces scientific, technical, and research documents where Mermaid diagrams are embedded directly in markdown as the source format. The bundled example report on CRISPR-Cas9 gene editing demonstrates standards: overview sections, quantified findings such as 78% mean editing efficiency in HEK293T cells, correlation notes, and diagrams rendered from Mermaid blocks. Developers reach for markdown-mermaid-writing when turning analysis results, lab workflows, or system designs into shareable reports that need both narrative prose and flowcharts, sequence diagrams, or process charts without separate drawing tools. Output targets publication-ready structure rather than casual notes.

  • Converts research findings and experimental workflows into structured markdown reports
  • Embeds production-quality Mermaid diagrams directly in markdown for flowcharts, timelines, and visualizations
  • Enforces consistent scientific reporting standards including go/no-go checkpoints and quantitative result sections
  • Produces self-contained documents optimized for both human readers and AI search engines

Markdown Mermaid Writing by the numbers

  • 985 all-time installs (skills.sh)
  • +44 installs in the week ending Jul 29, 2026 (Skillselion tracking)
  • Ranked #257 of 1,881 Documentation skills by installs in the Skillselion catalog
  • Security screen: LOW risk (skills.sh audit)
  • Data as of Jul 29, 2026 (Skillselion catalog sync)
npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill markdown-mermaid-writing

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Installs985
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Last updatedJuly 29, 2026
Repositoryk-dense-ai/scientific-agent-skills

How do you embed Mermaid diagrams in research markdown?

Generate publication-ready scientific, technical, and research documents that combine clear markdown prose with accurate, embedded Mermaid diagrams.

Who is it for?

Researchers and engineers documenting experiments, pipelines, or system flows who need markdown plus inline Mermaid diagrams in one artifact.

Skip if: Marketing social posts or Twitter Card meta tag work should use post-writer-sms or twitter-cards instead of scientific report formatting.

When should I use this skill?

A developer needs a scientific or technical report with Mermaid diagrams embedded in markdown from analysis notes or specifications.

What you get

Publication-ready markdown reports with embedded Mermaid diagrams, structured findings, and scientific narrative sections.

  • Markdown research reports
  • Embedded Mermaid diagrams

By the numbers

  • Example report cites 78% mean CRISPR editing efficiency in HEK293T cells
  • Example reports GC content 40–65% correlation with editing efficiency r = 0.82

Files

SKILL.mdMarkdownGitHub ↗

Markdown and Mermaid Writing

Overview

This skill teaches you — and enforces a standard for — creating scientific documentation using markdown with embedded Mermaid diagrams as the default and canonical format.

The core bet: a relationship expressed as a Mermaid diagram inside a .md file is more valuable than any image. It is text, so it diffs cleanly in git. It requires no build step. It renders natively on GitHub, GitLab, Notion, VS Code, and any markdown viewer. It uses fewer tokens than a prose description of the same relationship. And it can always be converted to a polished image later — but the text version remains the source of truth.

"The more you get your reports and files in .md in just regular text, which mermaid is
as well as being a simple 'script language'. This just helps with any downstream rendering
and especially AI generated images (using mermaid instead of just long form text to
describe relationships < tokens). Additionally mermaid can render along with markdown for
easy use almost anywhere by humans or AI."

>

— Clayton Young (@borealBytes), K-Dense Discord, 2026-02-19

When to Use This Skill

Use this skill when:

  • Creating any scientific document — reports, analyses, manuscripts, methods sections
  • Writing any documentation — READMEs, how-tos, decision records, project docs
  • Producing any diagram — workflows, data pipelines, architectures, timelines, relationships
  • Generating any output that will be version-controlled — if it's going into git, it should be markdown
  • Working with any other skill — this skill defines the documentation layer that wraps every other output
  • Someone asks you to "add a diagram" or "visualize the relationship" — Mermaid first, always

Do NOT start with Python matplotlib, seaborn, or AI image generation for structural or relational diagrams. Those are Phase 2 and Phase 3 — only used when Mermaid cannot express what's needed (e.g., scatter plots with real data, photorealistic images).

🎨 The Source Format Philosophy

Why text-based diagrams win

What mattersMermaid in MarkdownPython / AI Image
Git diff readable❌ binary blob
Editable without regenerating
Token efficient vs. prose✅ smaller❌ larger
Renders without a build step❌ needs hosting
Parseable by AI without vision
Works in GitHub / GitLab / Notion⚠️ if hosted
Accessible (screen readers)✅ accTitle/accDescr⚠️ needs alt text
Convertible to image later✅ anytime— already image

The three-phase workflow

flowchart LR
    accTitle: Three-Phase Documentation Workflow
    accDescr: Phase 1 Mermaid in markdown is always required and is the source of truth. Phases 2 and 3 are optional downstream conversions for polished output.

    p1["📄 Phase 1<br/>Mermaid in Markdown<br/>(ALWAYS — source of truth)"]
    p2["🐍 Phase 2<br/>Python Generated<br/>(optional — data charts)"]
    p3["🎨 Phase 3<br/>AI Generated Visuals<br/>(optional — polish)"]
    out["📊 Final Deliverable"]

    p1 --> out
    p1 -.->|"when needed"| p2
    p1 -.->|"when needed"| p3
    p2 --> out
    p3 --> out

    classDef required fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#1e3a5f
    classDef optional fill:#fef9c3,stroke:#ca8a04,stroke-width:2px,color:#713f12
    classDef output fill:#dcfce7,stroke:#16a34a,stroke-width:2px,color:#14532d

    class p1 required
    class p2,p3 optional
    class out output

Phase 1 is mandatory. Even if you proceed to Phase 2 or 3, the Mermaid source stays committed.

What Mermaid can express

Mermaid covers 24 diagram types. Almost every scientific relationship fits one:

Use caseDiagram typeFile
Experimental workflow / decision logicFlowchartreferences/diagrams/flowchart.md
Service interactions / API calls / messagingSequencereferences/diagrams/sequence.md
Data model / schemaER diagramreferences/diagrams/er.md
State machine / lifecycleStatereferences/diagrams/state.md
Project timeline / roadmapGanttreferences/diagrams/gantt.md
Proportions / compositionPiereferences/diagrams/pie.md
System architecture (zoom levels)C4references/diagrams/c4.md
Concept hierarchy / brainstormMindmapreferences/diagrams/mindmap.md
Chronological events / historyTimelinereferences/diagrams/timeline.md
Class hierarchy / type relationshipsClassreferences/diagrams/class.md
User journey / satisfaction mapUser Journeyreferences/diagrams/user_journey.md
Two-axis comparison / prioritizationQuadrantreferences/diagrams/quadrant.md
Requirements traceabilityRequirementreferences/diagrams/requirement.md
Flow magnitude / resource distributionSankeyreferences/diagrams/sankey.md
Numeric trends / bar + line chartsXY Chartreferences/diagrams/xy_chart.md
Component layout / spatial arrangementBlockreferences/diagrams/block.md
Work item status / task columnsKanbanreferences/diagrams/kanban.md
Cloud infrastructure / service topologyArchitecturereferences/diagrams/architecture.md
Multi-dimensional comparison / skills radarRadarreferences/diagrams/radar.md
Hierarchical proportions / budgetTreemapreferences/diagrams/treemap.md
Binary protocol / data formatPacketreferences/diagrams/packet.md
Git branching / merge strategyGit Graphreferences/diagrams/git_graph.md
Code-style sequence (programming syntax)ZenUMLreferences/diagrams/zenuml.md
Multi-diagram composition patternsComplex Examplesreferences/diagrams/complex_examples.md
💡 Pick the right type, not the easy one. Don't default to flowcharts for everything.
A timeline beats a flowchart for chronological events. A sequence beats a flowchart for
service interactions. Scan the table and match.

---

🔧 Core workflow

Step 1: Identify the document type

Check if a template exists before writing from scratch:

Document typeTemplate
Pull request recordtemplates/pull_request.md
Issue / bug / feature requesttemplates/issue.md
Sprint / project boardtemplates/kanban.md
Architecture decision (ADR)templates/decision_record.md
Presentation / briefingtemplates/presentation.md
Research paper / analysistemplates/research_paper.md
Project documentationtemplates/project_documentation.md
How-to / tutorialtemplates/how_to_guide.md
Status reporttemplates/status_report.md

Step 2: Read the style guide

Before writing any .md file: read references/markdown_style_guide.md.

Key rules to internalize:

  • One H1 per document — the title. Never more.
  • Emoji on H2 headings only — one emoji per H2, none in H3/H4
  • Cite everything — every external claim gets a footnote [^N] with full URL
  • Bold sparingly — max 2-3 bold terms per paragraph, never full sentences
  • Horizontal rule after every `</details>` — mandatory
  • Tables over prose for comparisons, configurations, structured data
  • Diagrams over walls of text — if it describes flow, structure, or relationships, add Mermaid

Step 3: Pick the diagram type and read its guide

Before creating any Mermaid diagram: read references/mermaid_style_guide.md.

Then open the specific type file (e.g., references/diagrams/flowchart.md) for the exemplar, tips, and copy-paste template.

Mandatory rules for every diagram:

accTitle: Short Name 3-8 Words
accDescr: One or two sentences explaining what this diagram shows.
  • No `%%{init}` directives — breaks GitHub dark mode
  • No inline `style` — use classDef only
  • One emoji per node max — at the start of the label
  • `snake_case` node IDs — match the label

Step 4: Write the document

Start from the template. Apply the markdown style guide. Place diagrams inline with related text — not in a separate "Figures" section.

Step 5: Commit as text

The .md file with embedded Mermaid is what gets committed. If you also generated a PNG or AI image, those are supplementary — the markdown is the source.

---

⚠️ Common pitfalls

Radar chart syntax (radar-beta)

WRONG:

radar
title Example
x-axis ["A", "B", "C"]
"Series" : [1, 2, 3]

CORRECT:

radar-beta
title Example
axis a["A"], b["B"], c["C"]
curve series["Series"]{1, 2, 3}
max 3
  • Use `radar-beta` not radar (the bare keyword doesn't exist)
  • Use `axis` to define dimensions, not x-axis
  • Use `curve` to define data series, not quoted labels with colon
  • No `accTitle`/`accDescr` — radar-beta doesn't support accessibility annotations; always add a descriptive italic paragraph above the diagram

XY Chart vs Radar confusion

DiagramKeywordAxis syntaxData syntax
XY Chart (bars/lines)xychart-betax-axis ["Label1", "Label2"]bar [10, 20] or line [10, 20]
Radar (spider/web)radar-betaaxis id["Label"]curve id["Label"]{10, 20}

Forgetting accTitle/accDescr on supported types

Only some diagram types support accTitle/accDescr. For those that don't, always place a descriptive italic paragraph directly above the code block:

_Radar chart comparing three methods across five performance dimensions. Note: Radar charts do not support accTitle/accDescr._
radar-beta
...

---

🔗 Integration with other skills

With scientific-schematics

scientific-schematics generates AI-powered publication-quality images (PNG). Use the Mermaid diagram as the brief for the schematic:

Workflow:
1. Create the concept as Mermaid in .md (this skill — Phase 1)
2. Describe the same concept to scientific-schematics for a polished PNG (Phase 3)
3. Commit both — the .md as source, the PNG as a supplementary figure

With scientific-writing

When scientific-writing produces a manuscript, all diagrams and structural figures should use this skill's standards. The writing skill handles prose and citations; this skill handles visual structure.

Workflow:
1. Use scientific-writing to draft the manuscript
2. For every figure that shows a workflow, architecture, or relationship:
   - Replace placeholder with a Mermaid diagram following this skill's guide
3. Use scientific-schematics only for figures that truly need photorealistic/complex rendering

With literature-review

Literature review produces summaries with lots of relationship data. Use this skill to:

  • Create concept maps (Mindmap) of the literature landscape
  • Show publication timelines (Timeline or Gantt)
  • Compare methodologies (Quadrant or Radar)
  • Diagram data flows described in papers (Sequence or Flowchart)

With any skill that produces output documents

Before finalizing any document from any skill, apply this skill's checklist:

  • [ ] Does the document use a template? If so, did I start from the right one?
  • [ ] Are all diagrams in Mermaid with accTitle + accDescr?
  • [ ] No %%{init}, no inline style, only classDef?
  • [ ] Are all external claims cited with [^N]?
  • [ ] One H1, emoji on H2 only?
  • [ ] Horizontal rules after every </details>?

---

📚 Reference index

Style guides

GuidePathLinesWhat it covers
Markdown Style Guidereferences/markdown_style_guide.md~733Headings, formatting, citations, tables, Mermaid integration, templates, quality checklist
Mermaid Style Guidereferences/mermaid_style_guide.md~458Accessibility, emoji set, color classes, theme neutrality, type selection, complexity tiers

Diagram type guides (24 types)

Each file contains: production-quality exemplar, tips specific to that type, and a copy-paste template.

references/diagrams/ — architecture, block, c4, class, complex\_examples, er, flowchart, gantt, git\_graph, kanban, mindmap, packet, pie, quadrant, radar, requirement, sankey, sequence, state, timeline, treemap, user\_journey, xy\_chart, zenuml

Document templates (9 types)

templates/ — decision\_record, how\_to\_guide, issue, kanban, presentation, project\_documentation, pull\_request, research\_paper, status\_report

Examples

assets/examples/example-research-report.md — a complete scientific research report demonstrating proper heading hierarchy, multiple diagram types (flowchart, sequence, gantt), tables, footnote citations, collapsible sections, and all style guide rules applied.

---

📝 Attribution

All style guides, diagram type guides, and document templates in this skill are ported from the SuperiorByteWorks-LLC/agent-project repository under the Apache-2.0 License.

  • Source: https://github.com/SuperiorByteWorks-LLC/agent-project
  • Author: Clayton Young / Superior Byte Works, LLC (@borealBytes)
  • License: Apache-2.0

This skill (as part of scientific-agent-skills) is distributed under the MIT License. The included Apache-2.0 content is compatible for downstream use with attribution retained, as preserved in the file headers throughout this skill.

---

[^1]: GitHub Blog. (2022). "Include diagrams in your Markdown files with Mermaid." https://github.blog/2022-02-14-include-diagrams-markdown-files-mermaid/

[^2]: Mermaid. "Mermaid Diagramming and Charting Tool." https://mermaid.js.org/

Related skills

How it compares

Use markdown-mermaid-writing for diagram-heavy research reports; use technical-writer for general API and product documentation without scientific report structure.

FAQ

What diagram format does markdown-mermaid-writing use?

markdown-mermaid-writing uses Mermaid syntax embedded directly in markdown as the source format for all diagrams. Flowcharts, process charts, and sequence diagrams live inside fenced Mermaid code blocks.

What kind of documents does markdown-mermaid-writing produce?

markdown-mermaid-writing produces publication-ready scientific and technical reports with structured overviews, quantified findings, and embedded Mermaid diagrams. The bundled CRISPR gene-editing example demonstrates the expected standard.

Is Markdown Mermaid Writing safe to install?

skills.sh reports 3 of 3 security scanners passed. Review the Security Audits panel on this page before installing in production.

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