lamm-mit/diagramming

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

# 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

{
  "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.