Scientific SchematicsSAFE

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

# Set your OpenRouter API key
export OPENROUTER_API_KEY='your_api_key_here'

# Generate any scientific diagram
python scripts/generate_schematic.py "CONSORT participant flow diagram" -o figures/consort.png

# Neural network architecture
python scripts/generate_schematic.py "Transformer encoder-decoder architecture" -o figures/transformer.png

# Biological pathway
python scripts/generate_schematic.py "MAPK signaling pathway" -o figures/pathway.png

# Get OpenRouter API key
# Visit: https://openrouter.ai/keys

# Set environment variable
export OPENROUTER_API_KEY='sk-or-v1-...'

# Or add to .env file
echo "OPENROUTER_API_KEY=sk-or-v1-..." >> .env

# Install Python dependencies (if not already installed)
pip install requests

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: scientific-schematics
description: "Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations."
allowed-tools: [Read, Write, Edit, Bash]
---

# Scientific Schematics and Diagrams

## Overview

Scientific schematics and diagrams transform complex concepts into clear visual representations for publication. **This skill uses Nano Banana Pro AI for diagram generation with Gemini 3 Pro quality review.**

**How it works:**
- Describe your diagram in natural language
- Nano Banana Pro generates publication-quality images automatically
- **Gemini 3 Pro reviews quality** against document-type thresholds
- **Smart iteration**: Only regenerates if quality is below threshold
- Publication-ready output in minutes
- No coding, templates, or manual drawing required

**Quality Thresholds by Document Type:**
| Document Type | Threshold | Description |
|---------------|-----------|-------------|
| journal | 8.5/10 | Nature, Science, peer-reviewed journals |
| conference | 8.0/10 | Conference papers |
| thesis | 8.0/10 | Dissertations, theses |
| grant | 8.0/10 | Grant proposals |
| preprint | 7.5/10 | arXiv, bioRxiv, etc. |
| report | 7.5/10 | Technical reports |
| poster | 7.0/10 | Academic posters |
| presentation | 6.5/10 | Slides, talks |
| default | 7.5/10 | General purpose |

**Simply describe what you want, and Nano Banana Pro creates it.** All diagrams are stored in the figures/ subfolder and referenced in papers/posters.

## Quick Start: Generate Any Diagram

Create any scientific diagram by simply describing it. Nano Banana Pro handles everything automatically with **smart iteration**:

```bash
# Generate for journal paper (highest quality threshold: 8.5/10)
python scripts/generate_schematic.py "CONSORT participant flow diagram with 500 screened, 150 excluded, 350 randomized" -o figures/consort.png --doc-type journal

# Generate for presentation (lower threshold: 6.5/10 - faster)
python scripts/generate_schematic.py "Transformer encoder-decoder architecture showing multi-head attention" -o figures/transformer.png --doc-type presentation

# Generate for poster (moderate threshold: 7.0/10)
python scripts/generate_schematic.py "MAPK signaling pathway from EGFR to gene transcription" -o figures/mapk_pathway.png --doc-type poster

# Custom max iterations (max 2)
python scripts/generate_schematic.py "Complex circuit diagram with op-amp, resistors, and capacitors" -o figures/circuit.png --iterations 2 --doc-type journal
```

**What happens behind the scenes:**
1. **Generation 1**: Nano Banana Pro creates initial image following scientific diagram best practices
2. **Review 1**: **Gemini 3 Pro** evaluates quality against document-type threshold
3. **Decision**: If quality >= threshold → **DONE** (no more iterations needed!)
4. **If below threshold**: Improved prompt based on critique, regenerate
5. **Repeat**: Until quality meets threshold OR max iterations reached

**Smart Iteration Benefits:**
- ✅ Saves API calls if first generation is good enough
- ✅ Higher quality standards for journal papers
- ✅ Faster turnaround for presentations/posters
- ✅ Appropriate quality for each use case

**Output**: Versioned images plus a detailed review log with quality scores, critiques, and early-stop information.

### Configuration

Set your OpenRouter API key:
```bash
export OPENROUTER_API_KEY='your_api_key_here'
```

Get an API key at: https://openrouter.ai/keys

### AI Generation Best Practices

**Effective Prompts for Scientific Diagrams:**

✓ **Good prompts** (specific, detailed):
- "CONSORT flowchart showing participant flow from screening (n=500) through randomization to final analysis"
- "Transformer neural network architecture with encoder stack on left, decoder stack on right, showing multi-head attention and cross-attention connections"
- "Biological signaling cascade: EGFR receptor → RAS → RAF → MEK → ERK → nucleus, with phosphorylation steps labeled"
- "Block diagram of IoT system: sensors → microcontroller → WiFi module → cloud server → mobile app"

✗ **Avoid vague prompts**:
- "Make a flowchart" (too generic)
- "Neural network" (which type? what components?)
- "Pathway diagram" (which pathway? what molecules?)

**Key elements to include:**
- **Type**: Flowchart, architecture diagram, pathway, circuit, etc.
- **Components**: Specific elements to include
- **Flow/Direction**: How elements connect (left-to-right, top-to-bottom)
- **Labels**: Key annotations or text to include
- **Style**: Any specific visual requirements

**Scientific Quality Guidelines** (automatically applied):
- Clean white/light background
- High contrast for readability
- Clear, readable labels (minimum 10pt)
- Professional typography (sans-serif fonts)
- Colorblind-friendly colors (Okabe-Ito palette)
- Proper spacing to prevent crowding
- Scale bars, legends, axes where appropriate

## When to Use This Skill

This skill should be used when:
- Creating neural network architecture diagrams (Transformers, CNNs, RNNs, etc.)
- Illustrating system architectures and data flow diagrams
- Drawing methodology flowcharts for study design (CONSORT, PRISMA)
- Visualizing algorithm workflows and processing pipelines
- Creating circuit diagrams and electrical schematics
- Depicting biological pathways and molecular interactions
- Generating network topologies and hierarchical structures
- Illustrating conceptual frameworks and theoretical models
- Designing block diagrams for technical papers

## How to Use This Skill

**Simply describe your diagram in natural language.** Nano Banana Pro generates it automatically:

```bash
python scripts/generate_schematic.py "your diagram description" -o output.png
```

**That's it!** The AI handles:
- ✓ Layout and com

SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.

What the source does

Filesystem

none-observed

Network

declared (1 observation(s))

Shell

none-observed

Dependencies

pinned

Secrets in source

none-found

Findings (4)

return base64.b64decode(base64_str)

return base64.b64decode(base64_str)

return base64.b64decode(base64_str)

# Set permanently (add to ~/.bashrc or ~/.zshrc)

Gates applied: no_behavioural_pass.