BioNetFlux: A Python Framework for Reaction--Diffusion--Chemotaxis Simulations on One-Dimensional Network Geometries

TL;DR

BioNetFlux is an open-source Python framework designed for simulating coupled PDE systems on one-dimensional network geometries, focusing on biological transport phenomena in microfluidic and vascular systems.

Contribution

It introduces a specialized simulation framework using Hybridized Discontinuous Galerkin methods tailored for biological networks on graph-like geometries.

Findings

Enables accurate modeling of transport phenomena in biological networks.

Supports complex geometries like microfluidic devices and vascular systems.

Provides an accessible tool for biological and biomedical research.

Abstract

We present BioNetFlux, an open-source Python framework for the numerical simulation of coupled systems of partial differential equations (PDEs) on one-dimensional multi-arc networks by the Hybridized Discontinuous Galerkin method. Its design targets biological transport phenomena on graph-like geometries that arise naturally in microfluidic organ-on-chip (OoC) devices, vascular networks, and in-vitro cell-migration assays.