Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add K-Dense-AI/scientific-agent-skills --skill markdown-mermaid-writinggit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/markdown-mermaid-writing)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/markdown-mermaid-writing"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/markdown-mermaid-writing/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/markdown-mermaid-writing"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/markdown-mermaid-writing.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk pass
- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00062 | $0.03806 |
| Opus 5.5 | $0.00025 | $0.01522 |
| Sonnet 5.5 | $0.00012 | $0.00761 |
| Haiku 4.5 | $0.00006 | $0.00381 |
Grade A, and why
markdown-mermaid-writing scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 26d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
8 near-identical copies found in the catalogue:
- markdown-mermaid-writing — 100% identical, 132 lines differ
- markdown-mermaid-writing — 100% identical, 127 lines differ
- markdown-mermaid-writing — 100% identical, 0 lines differ
- markdown-mermaid-writing — 100% identical, 131 lines differ
- markdown-mermaid-writing — 100% identical, 132 lines differ
- markdown-mermaid-writing — 100% identical, 132 lines differ
- markdown-mermaid-writing — 98% identical, 140 lines differ
- markdown-mermaid-writing — 97% identical, 138 lines differ
How it starts
The opening of the file, as written. The whole thing — 344 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Markdown and Mermaid Writing
Overview
This skill provides an optional house style for Markdown documentation with Mermaid structural diagrams. Follow the requested output format, existing repository conventions, and journal requirements first. This skill does not replace scientific analysis or plotting.
A relationship expressed as Mermaid inside a .md file is editable text that diffs
cleanly in git. A compatible host renders it without a separate user build step.
It renders where the host has Mermaid support; plain Markdown viewers may show only code,
and platforms/extensions ship different Mermaid versions. It uses
a compact source representation, though token use depends on the diagram. Exporting
SVG/PNG requires a renderer; retain the diagram source alongside exported figures.
"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:
- Writing a requested Markdown report, README, methods overview, or research note
- Diagramming a workflow, data pipeline, schema, state machine, or conceptual relationship
- Maintaining editable Mermaid sources and their rendered SVG/PNG exports
Use scientific plotting tools directly for measured data, uncertainty, statistical graphics, exact geometry, or publication figures that Mermaid cannot faithfully represent. Mermaid is not a required precursor to a quantitative chart or an existing SVG/code-native asset.
🎨 The Source Format Philosophy
Why text-based diagrams win
| What matters | Mermaid in Markdown | Python / AI Image |
|---|---|---|
| Git diff readable | ✅ text source | Plotting code/SVG can also be text |
| Editable source | ✅ | Plotting scripts and vector sources are editable |
| Compact relationship notation | Often | Depends on representation |
| Native preview | Host/version dependent | Viewer/format dependent |
| Parseable by AI without vision | ✅ | ❌ |
| Works in destination | Check Mermaid support and version | Check image format support |
| Accessible (screen readers) | Check SVG metadata and text alternative | Provide alt text/data table |
| Convertible to image later | ✅ anytime | — already image |
What ships with it
37 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- assets/examples/example-research-report.md 3.4 KB
- references/current-rendering.md 7.6 KB
- references/diagrams/architecture.md 5.0 KB
- references/diagrams/block.md 5.0 KB
- references/diagrams/c4.md 6.7 KB
- references/diagrams/class.md 8.6 KB
- references/diagrams/complex_examples.md 17 KB
- references/diagrams/er.md 8.0 KB
- references/diagrams/flowchart.md 7.0 KB
- references/diagrams/gantt.md 6.0 KB
- references/diagrams/git_graph.md 2.2 KB
- references/diagrams/kanban.md 4.0 KB
- references/diagrams/mindmap.md 2.5 KB
- references/diagrams/packet.md 2.4 KB
- references/diagrams/pie.md 1.9 KB
- references/diagrams/quadrant.md 2.6 KB
- references/diagrams/radar.md 2.8 KB
- references/diagrams/requirement.md 3.0 KB
- references/diagrams/sankey.md 2.6 KB
- references/diagrams/sequence.md 5.9 KB
- references/diagrams/state.md 5.7 KB
- references/diagrams/timeline.md 4.5 KB
- references/diagrams/treemap.md 2.6 KB
- references/diagrams/user_journey.md 5.2 KB
- references/diagrams/xy_chart.md 2.6 KB
- references/diagrams/zenuml.md 2.5 KB
- references/markdown_style_guide.md 32 KB
- references/mermaid_style_guide.md 27 KB
- templates/decision_record.md 7.2 KB
- templates/how_to_guide.md 7.1 KB
- templates/issue.md 12 KB
- templates/kanban.md 11 KB
- templates/presentation.md 8.1 KB
- templates/project_documentation.md 12 KB
- templates/pull_request.md 12 KB
- templates/research_paper.md 10 KB
- templates/status_report.md 7.2 KB
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 26d ago Changed · +13 lines · +2 tokens per session c28a9d602fc5
- 27d ago Changed · +8 lines f550a816184b
- 1mo ago First seen · 323 lines · 60 tokens per session scan A 801fabc81393
markdown-mermaid-writing is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (54,953 stars, last pushed yesterday), licensed MIT. It adds 62 tokens to every session and 3,806 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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