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Agent skill

Diagramming

by lamm-mit in lamm-mit/scienceclaw

Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows

Apache-2.0Auto-check passedDevelopment

Install Diagramming

skills CLI
$ npx skills add lamm-mit/scienceclaw --skill diagramming -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install lamm-mit/scienceclaw diagramming --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/diagramming .claude/skills/diagramming && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
diagramming
GitHub stars
244
Token cost
~487 tokens
SKILL.md length
76 words
Files
3 (incl. scripts)
Skills in repo
86
Repo updated
First seen
Licence
Apache-2.0

At a glance

Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows

  • Tasks that involve Diagrams
  • SKILL.md covers Overview, Usage and Output Format
  • Runs Python scripts from its folder; calls python3

What it does

Diagramming is an agent skill from lamm-mit/scienceclaw. Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows

Its SKILL.md is about 490 tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `scripts/diagram_generate.py`).

It sits in Development, covering Diagrams. It works with Mermaid. The licence is Apache-2.0.

When your agent uses it

  • Tasks that involve Diagrams

Example prompts

  • “/diagramming”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 2 files in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python3

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Diagramming loads about 487 tokens when it runs. Until then it costs about 27 tokens; SKILL.md has 76 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~27
When it runs · the whole SKILL.md, loaded when a task matches
~487

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 76 words, ~487 tokens.

Download SKILL.mdSave it as .claude/skills/diagramming/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.
name
diagramming
description
Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows

Overview

Generate technical diagrams using Mermaid syntax for biological pathways, molecular networks, experimental workflows, and research architecture. Outputs Mermaid code ready for rendering in GitHub, Notion, Obsidian, or any Mermaid-compatible renderer.

Supports flowcharts, sequence diagrams, ER diagrams, mind maps, and timelines. Generated diagrams can be saved as .mmd files or embedded directly in markdown documents.

Usage

bash
# Generate a flowchart of a drug discovery workflow
python3 skills/diagramming/scripts/diagram_generate.py \
  --type flowchart \
  --description "CRISPR gene editing workflow"

# Generate a mind map of a research topic
python3 skills/diagramming/scripts/diagram_generate.py \
  --type mindmap \
  --description "Alzheimer's disease molecular mechanisms"

# Generate a timeline and save to file
python3 skills/diagramming/scripts/diagram_generate.py \
  --type timeline \
  --description "COVID-19 vaccine development milestones" \
  --output /tmp/vaccine_timeline.mmd

# Generate an ER diagram for database schema
python3 skills/diagramming/scripts/diagram_generate.py \
  --type er \
  --description "genomics database schema with patients samples variants"

# Generate a sequence diagram
python3 skills/diagramming/scripts/diagram_generate.py \
  --type sequence \
  --description "antibody antigen binding mechanism"

Output Format

json
{
  "type": "flowchart",
  "mermaid_code": "graph TD\n  A[CRISPR gene editing workflow] --> B[Design gRNA]\n  B --> C[Validate Off-targets]\n  C --> D[Deliver to Cells]\n  D --> E[Verify Editing]\n  E --> F[Results]",
  "description": "CRISPR gene editing workflow"
}

Paste the mermaid_code into any Mermaid renderer or embed in markdown with triple backticks and mermaid language tag.

© lamm-mit, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 2 other files (scripts) in skills/diagramming of lamm-mit/scienceclaw.

  • SKILL.md
  • scripts/__pycache__/diagram_generate.cpython-313.pyc
  • scripts/diagram_generate.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

Diagramming next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Diagramming compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Diagramming this skilllamm-mit/scienceclaw244—~487Automated safety check: PassApache-2.0
Archify Diagramstt-a1i/archify81k—~2.9kAutomated safety check: PassMIT
Diagram Designcathrynlavery/diagram-design47k1 repos~7.5kAutomated safety check: PassMIT
Draw.io Diagram StudioAgents365-ai/drawio-skill10k—~2.4kAutomated safety check: NotesMIT
Pretty Mermaid Rendererimxv/Pretty-mermaid-skills1.5k—~2kAutomated safety check: PassMIT
Archify Diagram BuilderUnclecheng-li/AI_Animation1.5k2 repos~4.1kAutomated safety check: PassMIT

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Works with

Categories

Questions about Diagramming

What does Diagramming do?

Generate Mermaid diagrams for biological pathways, molecular networks, and experimental workflows. Diagramming is an agent skill from lamm-mit/scienceclaw.

When should I use Diagramming?

Diagramming fits situations like: tasks that involve Diagrams.

How do I install Diagramming in Claude Code?

Run `npx skills add lamm-mit/scienceclaw --skill diagramming -a claude-code`. Or copy the skill folder (skills/diagramming in lamm-mit/scienceclaw) into .claude/skills/diagramming in your project. Claude Code loads it when a task matches its description.

How do I install Diagramming in Codex?

Run `npx skills add lamm-mit/scienceclaw --skill diagramming -a codex`. Or copy the skill folder (skills/diagramming in lamm-mit/scienceclaw) into .agents/skills/diagramming in your project. Codex loads it when a task matches its description.

Can I use Diagramming in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add lamm-mit/scienceclaw --skill diagramming -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/diagramming, .gemini/skills/diagramming, .github/skills/diagramming and .opencode/skills/diagramming in your project.

What does Diagramming need to run?

Going by SKILL.md and its folder, Diagramming needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Diagramming access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Diagramming safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Diagramming use?

Diagramming is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Diagramming use?

About 487 tokens (SKILL.md is roughly 1.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Diagramming?

Skills that share tags, products or a category with Diagramming: Archify Diagrams (tt-a1i/archify, 81k stars), Diagram Design (cathrynlavery/diagram-design, 47k stars), Draw.io Diagram Studio (Agents365-ai/drawio-skill, 10k stars) and Pretty Mermaid Renderer (imxv/Pretty-mermaid-skills, 1.5k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Diagramming?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 86 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.