Protocol for an agent-based model of recombination in bacteria playing a public goods game

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory. For complete details on the use and execution of this protocol, please refer to Lee et al.1 [Display omitted] •An agent-based model is used to study cooperative behavior in bacterial populations•Modeling of homologous recombination in bacteria playing a public goods game•Implement the model in NetLogo and summarize the results using R language•Values of different population parameters and number of generations can be adjusted Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. Agent-based models are composed of individual agents coded for traits (e.g., cooperation and cheating) that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. The model is defined by the following variables: population size, population viscosity, cooperation multiplier, recombination rate, and fitness cost. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory.