Software
Here you’ll find software packages and tools I’ve developed for mathematical biology research. Each tool is designed to address specific challenges in modeling biological systems.
FunPy v0.1
A comprehensive Python toolbox for solving and analyzing integro-partial differential equations with built-in support for bifurcation analysis and continuation methods.
Key Features:
- Spectral collocation methods (Fourier series and Gegenbauer polynomials)
- Symbolic linearization capabilities
- Built-in continuation and bifurcation analysis tools
Technologies: Python NumPy SciPyTDR Solver
Finite volume solver for taxis-diffusion-reaction systems with support for non-local operators and the ROWMAP integrator.
Key Features:
- Finite volume discretization for taxis-diffusion-reaction equations
- Built-in support for non-local operators
- ROWMAP time integration for stiff systems
- Efficient handling of advection terms in biological models
Technologies: Python NumPy SciPyAdhesion Random Walk
Gillespie-SSA framework for simulating non-local space-jump processes, connecting microscopic cell behavior to macroscopic tissue patterns.
Key Features:
- Efficient Gillespie algorithm implementation for spatial systems
- Non-local jump process simulation
- Bridge between discrete stochastic and continuous models
- Analysis tools for pattern formation
Technologies: C++ Python