Agent-based model in biology

Agent-based models have many applications in biology, primarily due to the characteristics of the modeling method. Agent-based modeling is a rule-based, computational modeling methodology that focuses on rules and interactions among the individual components or the agents of the system. The goal of this modeling method is to generate populations of the system components of interest and simulate their interactions in a virtual world. Agent-based models start with rules for behavior and seek to reconstruct, through computational instantiation of those behavioral rules, the observed patterns of behavior. Several of the characteristics of agent-based models important to biological studies include:

Before the agent-based model can be developed, one must choose the appropriate software or modeling toolkit to be used. Madey and Nikolai provide an extensive list of toolkits in their paper "Tools of the Trade: A Survey of Various Agent Based Modeling Platforms". The paper seeks to provide users with a method of choosing a suitable toolkit by examining five characteristics across the spectrum of toolkits: the programming language required to create the model, the required operating system, availability of user support, the software license type, and the intended toolkit domain. Some of the more commonly used toolkits include Swarm,NetLogo, RePast, and Mason. Listed below are summaries of several articles describing agent-based models that have been employed in biological studies. The summaries will provide a description of the problem space, an overview of the agent-based model and the agents involved, and a brief discussion of the model results.

In the paper titled "Exploring Forest Management Practices Using an Agent-Based Model of Forest Insect Infestations", an agent-based model was developed to simulate attack behavior of the mountain pine beetle, Dendroctonus ponderosae, (MPB) in order to evaluate how different harvesting policies influence spatial characteristics of the forest and spatial propagation of the MPB infestation over time. About two-thirds of the land in British Columbia, Canada is covered by forests that are constantly being modified by natural disturbances such as fire, disease, and insect infestation. Forest resources make up approximately 15% of the province’s economy, so infestations caused by insects such as the MPB can have significant impacts on the economy. The MPB outbreaks are considered a major natural disturbance that can result in widespread mortality of the lodgepole pine tree, one of the most abundant commercial tree species in British Columbia. Insect outbreaks have resulted in the death of trees over areas of several thousand square kilometers.

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