Computational biology research — simulating developmental biology, gene regulatory networks, and neural interfaces.
Research goal: Understand and model biological development, epigenetic reprogramming, and the theoretical basis for AI-cognitive hybrid biological systems.
- Toggle switch (bistability — cell fate decisions)
- Repressilator (oscillation — biological clocks)
- Epigenetic state modeling
- Spatial developmental simulation (CompuCell3D)
- Neural circuit modeling (Brian2)
- Neural write interface simulation
Open in VS Code → "Reopen in Container" → everything installs automatically
pip install -r requirements.txtcd simulations/toggle-switch
python toggle_switch.pyMutual inhibition between two genes — the fundamental mechanism of cell fate decisions. When a stem cell "decides" to become a neuron vs a skin cell, this is the circuit doing it.
Three-gene oscillator ring — the mechanism behind circadian rhythms and developmental timing clocks.
| Layer | Library | Purpose |
|---|---|---|
| GRN simulation | Tellurium + Antimony | Gene regulatory networks |
| Stochastic | GillesPy2 | Noise/randomness in small cell populations |
| Spatial | CompuCell3D | Multicellular development |
| Neural | Brian2 | Neuron/circuit modeling |
| Scientific | NumPy, SciPy | Core math |
| Notebooks | JupyterLab | Exploration + visualization |
- Gardner et al. (2000) — Toggle switch: Nature 403:339-342
- Elowitz & Leibler (2000) — Repressilator: Nature 403:335-338
- Wolpert — Principles of Development (textbook foundation)
- Yamanaka (2006) — Induced pluripotency / epigenetic reprogramming (Nobel 2012)