Software

InPartS (Interacting Particle Simulations) is our primary framework for agent-based simulations of interacting cells and particles. It underpins nearly all of our particle-resolved studies of growing and dividing multicellular systems, in two and three dimensions.

It handles proliferating and dividing cells, motile active particles, mixed co-cultures, and arbitrary confining geometries, and is distributed as a suite of composable packages (core engine, a library of biological models, interactive visualization, and complex obstacles). Built in Julia for both high performance and accessibility, it has enabled even Bachelor’s and Master’s students to lead publications.

A framework for stochastic simulations of reaction systems with arbitrary internal rate dependencies and discrete-event delays, going beyond standard mass-action kinetics. It builds on the Gillespie algorithm with variants optimized for large, weakly connected reaction networks, and was released alongside our COVID-19 containment study.

The simulation and analysis code accompanying our study on local COVID-19 containment measures. It combines time-resolved estimation of the reproduction number from empirical data with stochastic spatial simulations of epidemic spread under locally and globally applied restrictions, reproducing all figures from the published manuscript.

MediaSim is a high-performance framework for reaction–diffusion systems and excitable media, optimized for multi-core CPUs and GPUs. It has been used for large-scale simulations of cardiac arrhythmias in realistic 3D heart geometries, spatiotemporal chaos, and epidemic spread, and is described in the monograph Complex Structure and Dynamics of the Heart (Springer, 2015). A standalone open-source release is in preparation.