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: Modular structure: The behavior of an agent-based model is defined by the rules of its agents. Existing agent rules can be modified or new agents can be added without having to modify the entire model. Emergent properties: Through the use of the individual agents that interact locally with rules of behavior, agent-based models result in a synergy that leads to a higher level whole with much more intricate behavior than those of each individual agent. Abstraction: Either by excluding non-essential details or when details are not available, agent-based models can be constructed in the absence of complete knowledge of the system under study. This allows the model to be as simple and verifiable as possible. Stochasticity: Biological systems exhibit behavior that appears to be random. The probability of a particular behavior can be determined for a system as a whole and then be translated into rules for the individual agents.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.