ya||a: GPU-powered Spheroid Models for Mesenchyme and Epithelium

Abstract

ya||a is yet another parallel agent-based model for morphogenesis. It is several orders of magnitude faster than conventional models, because it runs on GPUs and because it has been designed for performance: Previously only complex and therefore computationally expensive models could simulate both mesenchyme and epithelium. We chose to extend the simple spheroid model by the addition of spin-like polarities to simulate epithelial sheets and tissue polarity. We also incorporate recently developed models for protrusions and migration. ya||a is written in concise, plain CUDA/C++ and available at github dot com/germannp/yalla under the MIT license.