| name | markdown-mermaid-writing |
| description | Comprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization. Establishes text-based diagrams as the default documentation standard with full style guides (markdown + mermaid), 24 diagram type references, and 9 document templates. |
| allowed-tools | Read Write Edit Bash |
| license | Apache-2.0 |
| metadata | version: "1.1" skill-author: Clayton Young / Superior Byte Works, LLC (@borealBytes) skill-source: https://github.com/SuperiorByteWorks-LLC/agent-project skill-version: "1.0.0" skill-contributors: "Clayton Young (Superior Byte Works, LLC / @borealBytes; Author and originator); K-Dense Team (K-Dense Inc.; Integration target and community feedback)" |
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 matters | Mermaid in Markdown | Python / 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 case | Diagram type | File |
|---|
| Experimental workflow / decision logic | Flowchart | references/diagrams/flowchart.md |
| Service interactions / API calls / messaging | Sequence | references/diagrams/sequence.md |
| Data model / schema | ER diagram | references/diagrams/er.md |
| State machine / lifecycle | State | references/diagrams/state.md |
| Project timeline / roadmap | Gantt | references/diagrams/gantt.md |
| Proportions / composition | Pie | references/diagrams/pie.md |
| System architecture (zoom levels) | C4 | references/diagrams/c4.md |
| Concept hierarchy / brainstorm | Mindmap | references/diagrams/mindmap.md |
| Chronological events / history | Timeline | references/diagrams/timeline.md |
| Class hierarchy / type relationships | Class | references/diagrams/class.md |
| User journey / satisfaction map | User Journey | references/diagrams/user_journey.md |
| Two-axis comparison / prioritization | Quadrant | references/diagrams/quadrant.md |
| Requirements traceability | Requirement | references/diagrams/requirement.md |
| Flow magnitude / resource distribution | Sankey | references/diagrams/sankey.md |
| Numeric trends / bar + line charts | XY Chart | references/diagrams/xy_chart.md |
| Component layout / spatial arrangement | Block | references/diagrams/block.md |
| Work item status / task columns | Kanban | references/diagrams/kanban.md |
| Cloud infrastructure / service topology | Architecture | references/diagrams/architecture.md |
| Multi-dimensional comparison / skills radar | Radar | references/diagrams/radar.md |
| Hierarchical proportions / budget | Treemap | references/diagrams/treemap.md |
| Binary protocol / data format | Packet | references/diagrams/packet.md |
| Git branching / merge strategy | Git Graph | references/diagrams/git_graph.md |
| Code-style sequence (programming syntax) | ZenUML | references/diagrams/zenuml.md |
| Multi-diagram composition patterns | Complex Examples | references/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 type | Template |
|---|
| Pull request record | templates/pull_request.md |
| Issue / bug / feature request | templates/issue.md |
| Sprint / project board | templates/kanban.md |
| Architecture decision (ADR) | templates/decision_record.md |
| Presentation / briefing | templates/presentation.md |
| Research paper / analysis | templates/research_paper.md |
| Project documentation | templates/project_documentation.md |
| How-to / tutorial | templates/how_to_guide.md |
| Status report | templates/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
| Diagram | Keyword | Axis syntax | Data syntax |
|---|
| XY Chart (bars/lines) | xychart-beta | x-axis ["Label1", "Label2"] | bar [10, 20] or line [10, 20] |
| Radar (spider/web) | radar-beta | axis 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:
📚 Reference index
Style guides
| Guide | Path | Lines | What it covers |
|---|
| Markdown Style Guide | references/markdown_style_guide.md | ~733 | Headings, formatting, citations, tables, Mermaid integration, templates, quality checklist |
| Mermaid Style Guide | references/mermaid_style_guide.md | ~458 | Accessibility, 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.
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.
