Simulating microbial communities' evolution via Agent base modelling: a Python tool

In this work, we blueprint a Dashboard that allows users to simulate the bacterial community's evolution through an intuitive GUI. The underlying Python-coded simulator implements an agent-based model of bacterial species, nutrients, and environment, allowing full customization and upgradability of the tool, due to its intrinsic modularity. Specifically, the model aims to represent discretized spaces, hosting a certain number of bacteria for each species and a defined amount of nutrients characterizing the surrounding environment. Bacteria can migrate from one spatial unit into another, looking for different nutrients (i.e., metabolites) across the whole space path. Growth and survival are governed by bacterial metabolisms, which are in turn functions of the metabolites present in each specific spatial unit at a certain time. Thus, our tool simulates how bacteria consume and produce metabolites, following species-specific metabolism rules, letting the system dynamically evolve through bacterial growth, death, spatial migration, and continuous updates of the available metabolite pool.