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Abstract
PhysiCell for Kidney FTU
This app simulates a PhysiCell model for the kidney functional tissue unit (FTU) which is part of HuBMAP project.
To see the full spatial model, use the default initial conditions, i.e., select the "all cells" at the bottom of the Config Basics tab. Since the spatial model is fairly symmetric, to speed up a simulation, select the "cells y>0" option to see only the upper half of the cell population.
Select the Run tab, and click "Run Simulation". The simulation's terminal output will appear in that tab. Once the simulation is done (or even before it completes), select the "Plot" tab and click "Play" to see the visual results of the simulation. Be patient for the results to appear, especially with the "all cells" option.
This model and cloud-hosted demo are part of a course on computational multicellular systems biology created and taught by
Dr. Paul Macklin in the Department of Intelligent Systems Engineering at Indiana University. It is also part of the education
and outreach for the IU Engineered nanoBIO Node and the NCI-funded cancer systems biology grant U01CA232137.
The models are built using PhysiCell, a C++ framework for multicellular systems biology [1].
Publications
Ghaffarizadeh A, Heiland R, Friedman SH, Mumenthaler SM, Macklin P (2018) PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems. PLoS Comput Biol 14(2): e1005991. https://doi.org/10.1371/journal.pcbi.1005991
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