A Framework for Individual-based Simulation of Heterogeneous Cell Populations

• Main Author: Abdennur, Nezar A
• Other Authors: Kaern, Mads
• Language: en
• Published: Université d'Ottawa / University of Ottawa 2011
• Subjects: simulation; computational biology; individual-based models; systems biology; population dynamics; object-oriented; constant-number monte carlo; stochastic chemical kinetics; cell physiology; simulation channels; scheduling protocols; cell populations; population heterogeneity; differential reproduction; noise; heritability; dynamics; cell lineages
• Online Access: http://hdl.handle.net/10393/20478; http://dx.doi.org/10.20381/ruor-5079

An object-oriented framework is presented for developing and simulating individual-based models of cell populations. The framework supplies classes to define objects called simulation channels that encapsulate the algorithms that make up a simulation model. These may govern state-updating events at the individual level, perform global state changes, or trigger cell division. Simulation engines control the scheduling and execution of collections of simulation channels, while a simulation manager coordinates the engines according to one of two scheduling protocols. When the ensemble of cells being simulated reaches a specified maximum size, a procedure is introduced whereby random cells are ejected from the simulation and replaced by newborn cells to keep the sample population size constant but representative in composition. The framework permits recording of population snapshot data and/or cell lineage histories. Use of the framework is demonstrated through validation benchmarks and two case studies based on experiments from the literature.