Cell populations simulated in silico within SimulCell accurately reproduce the behaviour of experimental cell cultures

Abstract

In silico simulations are used to understand cell behaviour by means of different approaches and tools, which range from reproducing average population trends to building lattice-based models to, more recently, creating populations of individual cell agents whose mass, volume and morphology behave according to more or less precise rules and models. In this work, a new agent-based simulator, SimulCell, was conceived, developed and used to predict the behaviour of eukaryotic cell cultures while growing attached to a flat surface. The system, starting from time-lapse microscopy experiments, uses growth, proliferation and migration models to create synthetic populations closely resembling original cultures. Support for cell-cell and cell-environment interaction makes cell agents able to react to changes in medium composition and other events, such as physical damage or chemical modifications occurring in the culture plate. The simulator is accessible through a web application and generates data that can be shown as tables and graphs or exported for further analyses.