Computational rule-based model of the LDL receptor system using PyBioNetGen.
# 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.
├── models/ # PyBioNetGen model code
├── scripts/ # Analysis pipeline
├── data/ # Variant functional scores
├── results/ # Figures and simulation data
└── docs/ # Documentation
- 1-Week Plan - Project timeline
- PyBioNetGen - Rule-based modeling in Python
- Python 3.8+ - Core language
- pandas/numpy/scipy - Data analysis
- matplotlib/seaborn - Visualization
Based on: Tabet et al., Science 2025 - "The functional landscape of coding variation in the familial hypercholesterolemia gene LDLR"
MIT License