Micro-scale modelling of microbial communities using Individual-based Models

Individual-based Models (IbM) are one of the most promising frameworks to study microbial communities, as they can explicitly describe the behaviour of each cell. The development of a general-purpose IbM solver should focus on efficiency and flexibility due to the unique characteristics of microbial systems. However, available tools for these purposes present significant limitations. Most of them only facilitate serial computing for single simulation, or only focus on biological processes, but do not model mechanical and chemical processes in detail. We developed the NUFEB IbM solver that addresses some of these shortcomings. The tool facilitates the modelling of much needed biological, chemical, physical and individual microbes in detail, and offers the flexibility of model extension and customisation. It is also fully parallelised and allows for the simulation of large complex microbial system. In the talk, I will give an overview of NUFEB solver's functionalities and implementation details, and provide examples that illustrate the type of microbial systems it can be used to model and simulate.