PhenoCellPy: A Python package for biological cell behavior modeling

Juliano Ferrari Gianlupi

Indiana University

"PhenoCellPy: A Python package for biological cell behavior modeling"

PhenoCellPy is an open-source Python package that 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 supports integration with modeling frameworks in a number of ways, e.g. by messaging the main simulation when a change in behavior occurs. PhenoCellPy can function with any python-based modeling framework that supports Python 3, NumPy and SciPy.
Additional authors: T.J. Sego, Department of Medicine, University of Florida, Gainesville, FL, USA; James P. Sluka, Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University Bloomington, Bloomington, IN, USA; James A. Glazier, Department of Intelligent Systems Engineering and Biocomplexity Institute, Indiana University Bloomington, Bloomington, IN, USA

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