Early PhysiCell test: a 3-D tumor simulation with 500k cells




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Published on Aug 15, 2016

This is 2013 test of a PhysiCell prototype, simulating growth of a hanging drop tumor spheroid up to 500,000 cells on a dual 6-core machine. The 24-threaded simulation required about 89 hours, including file I/O time to save simulation data once per simulated hour.

This test was featured in our preprint here:


Dark circles: cell nuclei
Green cells: Proliferating Ki67+ cells
Pale blue cells: Quiescent Ki67- cells
Red cells: Apoptotic cells (cleaved Caspase-3 positive)
Brown cells: Necrotic cells

Demonstration of PhysiCell, an agent-based, lattice-free model. Cell velocities determined by balance of adhesive and repulsive forces. Each cell has a phenotypic state governed by stochastic processes derived from nonhomogeneous Poisson processes. PhysiCell is available as open source at http://PhysiCell.MathCancer.org and http://PhysiCell.sf.net.

Source: Ghaffarizadeh et al., PhysiCell: an open source physics-based cell simulator for 3-D multicellular systems, PLoS Comput. Biol., 2016 (in submission).

Open access: [not yet available]


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