A cell-centered, agent-based framework that enables flexible environment granularities. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Kennedy, Ryan; Ropella, Glen; Hunt, C
• Is Part Of: Theoretical biology and medical modelling. Volume 13:Issue 1(2016)
• Page Start: 1
• Page End: 14
• Publication Date: 2016-12
• Subjects: Biomimetic -- Cell behavior -- Off-Lattice -- Delaunay -- Voronoi -- Morphogenesis -- Mechanistic explanations -- Modeling; Biology -- Mathematical models -- Periodicals; Biology -- Periodicals; Medical sciences -- Periodicals; 570.15118
• DOI: 10.1186/s12976-016-0030-9
• Languages: English
• ISSNs: 1742-4682

Abstract

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.