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Abstract
Basic instructions
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.
Powered by
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.
See http://PhysiCell.MathCancer.org.
The Jupyter-based GUI was auto-generated by xml2jupyter [3], a technique to create graphical user interfaces for command-line scientific applications.
Bio
To learn more about our work, please visit MathCancer.org.
Credits
Scientific Staff
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)
Sponsored by
- 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
References
[1] 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
[2] 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
[3] 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