LDLR Functional Landscape Modeling

Computational rule-based model of the LDL receptor system using PyBioNetGen.

Quick Start

# Setup
python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt

# Run simulations
python scripts/run_variants.py

# Analyze results
python scripts/analyze_results.py

Project Structure

.
├── models/          # PyBioNetGen model code
├── scripts/         # Analysis pipeline
├── data/            # Variant functional scores
├── results/         # Figures and simulation data
└── docs/            # Documentation

Documentation

• 1-Week Plan - Project timeline

Technology

• PyBioNetGen - Rule-based modeling in Python
• Python 3.8+ - Core language
• pandas/numpy/scipy - Data analysis
• matplotlib/seaborn - Visualization

Citation

Based on: Tabet et al., Science 2025 - "The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR"

License

MIT License