PhenoCellPy: A Python package for biological cell behavior modeling

Abstract

AbstractPhysiCell, a mechanistic center-based agent-based modeling framework, describes sequences of cell behaviors in a very elegant way with its phenotype submodel. However, its phenotypes are not usable in other frameworks, and the creation of a new phenotype is not straight forward. PhenoCellPy is an open-source Python package that implements PhysiCell’s phenotypes and their methods in a general way, that is easily extended and embedded into other python-based models. PhenoCellPy defines methods for modeling sequences of cell behaviors and states (e.g., the cell cycle, or the Phases of cellular necrosis). PhenoCellPy defines Python classes for the Cell Volume (which it subdivides between the cytoplasm and nucleus) and its evolution, the state of the cell and the behaviors the cell displays in each state (called the Phase), and the sequence of behaviors (called the Phenotype). PhenoCellPy’s can extend existing modeling frameworks as an embedded model. It integrates with the frameworks by defining the cell states (phases), signaling when a state change occurs, if division occurs, and by receiving information from the framework (e.g., how much interferon the cell is exposed to). PhenoCellPy can function with any python-based modeling framework that supports Python 3, NumPy and SciPy.