Agent-Based Modeling of Host-Pathogen Systems: The Successes and   Challenges
  Agent-based models have been employed to describe numerous processes in immunology. Simulations based on these types of models have been used to enhance our understanding of immunology and disease pathology. We review various agent-based models relevant to host-pathogen systems and discuss their contributions to our understanding of biological processes. We then point out some limitations and challenges of agent-based models and encourage efforts towards reproducibility and model validation. 
Amy L. Bauer, Catherine A.A. Beauchemin, and Alan S. Perelson