This is the home of the future user guide for PhysiCell.
This user guide will teach you how to download and use PhysiCell, as well as document the key classes and functions. Wherever possible, it will demonstrate with specific examples. Please note that this guide will be periodically updated. Users should check PhysiCell.MathCancer.org for the latest version. The PhysiCell method paper was published in PLoS Computational Biology.
If you use PhysiCell, please cite it as:
We implemented and solved our model using PhysiCell (Version 1.10.2) [1].
[1] A. Ghaffarizadeh, R. Heiland, S.H. Friedman, S.M. Mumenthaler and P. Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for 3-D Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991.
Because PhysiCell makes extensive use of BioFVM, we suggest you also cite it:
We implemented and solved the model using PhysiCell (Version 1.10.2) [1], with BioFVM [2] to solve the transport equations.
[1] A Ghaffarizadeh, R Heiland, SH Friedman, SM Mumenthaler, and P Macklin. PhysiCell: an Open Source Physics-Based Cell Simulator for Multicellular Systems, PLoS Comput. Biol. 14(2): e1005991, 2018. DOI: 10.1371/journal.pcbi.1005991
[2] A Ghaffarizadeh, SH Friedman, and P Macklin. BioFVM: an efficient parallelized diffusive transport solver for 3-D biological simulations, Bioinformatics 32(8): 1256-8, 2016. DOI: 10.1093/bioinformatics/btv730
Please remember: if you use an additional addon, please make sure to cite it, too! This is critical for scientific rigor (to correctly document your method), reproducibility, and good academic behavior. We have started testing methods to auto-generate suggested citations for addons; see the auto-generated CITATION.txt when you run your model. This will be further developed in future versions of PhysiCell.