MorphoGrad: A MATLAB toolbox for simulating steady-state morphogen gradients under cell-to-cell variability

Studying morphogen gradient-based tissue patterning in silico while accounting for biological variability remains challenging. Here, we present a MATLAB-based protocol for simulating steady-state morphogen gradients in one- and two-dimensional tissues with cell-to-cell variability in model parameters. We describe steps for configuring cell-based geometries, defining reaction-diffusion equations and model parameters, assigning stochastic parameter variability, setting boundary conditions and solver options, running simulations, and analyzing stochastic gradients to quantify patterning precision. For complete details on the use and execution of this protocol, please refer to Long et al.¹.