Abstract
Multicellular simulations of tumor growth in complex 3-D tissues, where data come from high content in vitro and bioengineered experiments, have gained significant attention by the cancer modeling community in recent years. Agent-based models are often selected for these problems because they can directly model and track cells’ states and their interactions with the microenvironment. We describe PhysiCell, a specific agent-based model that includes cell motion, cell cycling, and cell volume changes. The model has been performance tested on systems of 105 cells on desktop computers, and is expected to scale to 106 or more cells on single super-computer compute nodes. We plan an open source release of the software in early 2016 at PhysiCell.MathCancer.org
Footnotes
Research supported by the Breast Cancer Research Foundation and the National Cancer Institute (R01CA180149, 5U54CA143907).
A. Ghaffarizadeh, S. H. Friedman, and P. Macklin are with the Center for Applied Molecular Medicine, Department of Medicine, University of Southern California, 2250 Alcazar St., HSC-CSC 240, Los Angeles, CA 90033-9075, USA. E-mail: {aghaffar, samuelf, paul.macklin}@usc.edu. P. Macklin is the corresponding author (Tel: (310) 701-5785).