GRNDynamics

Gene Regulatory Network Dynamics Simulator — attractor analysis, ODE simulation, and Waddington landscape visualization.

Quick Start

pip install numpy scipy pandas plotly networkx matplotlib scikit-learn --break-system-packages -q
python3 demo.py

Three Modeling Frameworks

1. Boolean Network Dynamics — exhaustive attractor search for N≤22 genes
2. ODE Continuous Dynamics — Hill-function-based simulation with adaptive RK4 integration
3. Network Inference — ARACNE (mutual information) and GENIE3 (random forest) from expression data

Demos

• demo.py --network pluripotency — OCT4-SOX2-NANOG pluripotency GRN (6 genes)
• demo.py --network emt — EMT transition circuit (8 genes, tristable)
• demo.py --network cell_cycle — Mammalian cell cycle G1/S switch (9 genes)