title: A cell-centered, agent-based framework that enables flexible environment granularities.
abstract: BACKGROUND
  Mechanistic explanations of cell-level phenomena typically adopt an observer perspective. Explanations developed from a cell's perspective may offer new insights. Agent-based models lend themselves to model from an individual perspective, and existing agent-based models generally utilize a regular lattice-based environment. A framework which utilizes a cell's perspective in an off-lattice environment could improve the overall understanding of biological phenomena.
  
  
  RESULTS
  We present an agent-based, discrete event framework, with a demonstrative focus on biomimetic agents. The framework was first developed in 2-dimensions and then extended, with a subset of behaviors, to 3-dimensions. The framework is expected to facilitate studies of more complex biological phenomena through exploitation of a dynamic Delaunay and Voronoi off-lattice environment. We used the framework to model biological cells and to specifically demonstrate basic biological cell behaviors in two- and three-dimensional space. Potential use cases are highlighted, suggesting the utility of the framework in various scenarios.
  
  
  CONCLUSIONS
  The framework presented in this manuscript expands on existing cell- and agent-centered methods by offering a new perspective in an off-lattice environment. As the demand for biomimetic models grows, the demand for new methods, such as the presented Delaunay and Voronoi framework, is expected to increase.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
authors.forename: Ryan C
authors.initials: RC
authors.lastname: Kennedy
authors.affiliation: Tempus Dictum, Inc., Milwaukie, OR, USA.
authors.forename: Glen Ep
authors.initials: GE
authors.lastname: Ropella
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA. a.hunt@ucsf.edu.
authors.forename: C Anthony
authors.initials: CA
authors.lastname: Hunt
mesh_terms: D032701:Biomimetics / Q000379:methods*; D002467:Cell Nucleus / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D004847:Epithelial Cells / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D012984:Software
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