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. This page is still under construction more to come soon.
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