This tool version is unpublished and cannot be run. If you would like to have this version staged, you can put a request through HUB Support.
Modify the parameters in the "config basics" and "user params" tabs. Click the "run" button once ready.
To view the cell plots, click the "cell plots" tab, and slide the bar to advance through simulation frames. Note that as the simulation runs, the "max" field (maximum frame number) will increase, so you can view more simulation frames.
To view the tracer field, click the "substrate plots" tab and slide through the saved times. Note that as the simulation runs, the "max" field (maximum frame number) will increase, so you can view more simulation frames.
This software is powered by PhysiCell [1-2], a powerful simulation tool that combines multi-substrate diffusive transport and off-lattice cell models. PhysiCell is BSD-licensed, and available at:
- GitHub releases: https://github.com/MathCancer/PhysiCell/releases
- SourceForge downloads: https://sourceforge.net/projects/physicell/
It is a C++, cross-platform code with minimal software dependencies. It has been tested and deployed in Linux, BSD, OSX, Windows, and other environments, using the standard g++ compiler.
The Jupyter-based GUI was auto-generated by xml2jupyter , a technique to create graphical user interfaces for command-line scientific applications.
To learn more about our work, please visit MathCancer.org.
Randy Heiland, Research Associate, Intelligent Systems Engineering, Indiana University.
- Lead software architect
Paul Macklin, Ph.D. , Associate Professor, Intelligent Systems Engineering, Indiana University.
- Scientific lead, developed PhysiCell simulation model
The following undergraduate students have contributed to this project:
Jupyter notebook and UI development
- Eric Bower (IU Intelligent Systems Engineering, B.S., 2018-present)
- Daniel Mishler (IU Intelligent Systems Engineering, B.S., 2018-present)
- Tyler Zhang (IU Intelligent Systems Engineering, B.S., 2018)
- NSF EEC-1720625. Network for Computational Nanotechnology - Engineered nanoBIO Node
- Breast Cancer Research Foundation
- Jayne Koskinas Ted Giovanis Foundation for Health and Policy
- NIH U01CA232137
 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
 Ghaffarizadeh A, Friedman SH, Macklin P (2016) BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics 32(8):1256-8. https://doi.org/10.1093/bioinformatics/btv730
 Heiland R, Mishler D, Zhang T, Bower E, Macklin P (2019, in preparation) Xml2jupyter: Mapping parameters between XML and Jupyter widgets. J Open Source Software.
Cite this work
Researchers should cite this work as follows:
This tool is still in preparation for submission. For now, please cite:
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