Citing PhysiCell

PhysiCell method citation

If you use PhysiCell in your project, please cite the original method paper in PLoS Computational Biology:

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.

Suggestion

Suppose you used PhysiCell Version 1.14.1 in your work. We suggest a sentence like this in your Method section:

We used PhysiCell Version 1.14.1 to build an agent-based simulation model (Ghaffarizadeh et al., 2018).

Basic PhysiCell method description

For writing your method section, you may want a basic description of the PhysiCell framework. Please consider quoting a brief description we have used.

As briefly summarized by Rocha et al. (2024), "PhysiCell is an open-source framework that allows the development of multicellular models at various spatial/temporal scales. In this tool, the cells are represented by off-lattice agents with independent behaviors, including cell cycle progression, death processes, volume changes, and motility. Some of these dynamics may be defined by substrate availability in the environment, which is represented on PhysiCell using an open-source biological diffusion solver, BioFVM (Ghaffarizadeh et al., 2016). PhysiCell has been used in a wide variety of multicellular problems, such as virus therapy, cancer immunology, tissue mechanics, and drug screening, among others (Ozik et al., 2019; Getz et al., 2021; Rocha et al., 2021; Wang et al., 2021;Jenner et al., 2020)."

This description references:

H.L. Rocha et al., A multiscale model of immune surveillance in micrometastases gives insights on cancer patient digital twins. npj Syst Biol Appl 10, 144 (2024). doi: 10.1038/s41540-024-00472-z.
A. Ghaffarizadeh et al., BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations, Bioinformatics 32(8): 1256-8 (2016). doi: 10.1093/bioinformatics/btv730.
J. Ozik et al., P. Learning-accelerated discovery of immune-tumour interactions. Mol. Syst. Des. Eng. 4: 747-760 (2019). doi: 10.1039/C9ME00036D
M. Getz et al., Iterative community-driven development of a sars-cov-2 tissue simulator, bioRxiv 2020.04.02.019075 (2021); doi: 10.1101/2020.04.02.019075
H.L. Rocha et al., A persistent invasive phenotype in post-hypoxic tumor cells is revealed by fate mapping and computational modeling. iScience 24: 102935 (2021). doi: 10.1016/j.isci.2021.102935.
Y. Wang et al., Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach. Sci. Rep. 11: 1-20 (2021). doi: 10.1038/s41598-020-78780-7
A. Jenner et al., Engineering in medicine to address the challenge of cancer drug resistance: from micro-and nanotechnologies to computational and mathematical modeling. Chem. Rev. 121: 3352-89 (2020). doi: 10.1016/j.isci.2022.104395.

Adding citations of PhysiCell extensions

Citations for PhysiCell rules / grammar

If you used the modeling grammar / language to construct your simulation model, please cite its recent preprint in addition to PhysiCell:

J.A.I. Johnson et al., Digitize your Biology! Modeling multicellular systems through interpretable cell behavior. bioRxiv 2023.09.17.557982 (2024); doi: 10.1101/2023.09.17.557982.

Suggestion

We suggest you add a sentence just after citing PHysiCell, such as:

We used PhysiCell Version 1.14.1 to build an agent-based simulation model (Ghaffarizadeh et al., 2018). We developed our model rules using the Cell Behavior Hypothesis Grammar (Johnson et al.).

Citations for PhysiCell Studio (including PhysiCell Cloud)

If you used PhysiCell Studio to build, explore, and/or visualize your model, please cite its method paper in addition to PhysiCell:

Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass, Heber Lima da Rocha, Marco Ruscone, Vincent Noël, and Paul Macklin, PhysiCell Studio: a graphical tool to make agent-based modeling more accessible. Gigabyte, 2024. doi: 10.46471/gigabyte.128.

Suggestion

We suggest you refine the basic citation to reference PhysiCell Studio, such as:

We used PhysiCell Version 1.14.1 (Ghaffarizadeh et al., 2018) to build an agent-based simulation model, with interactive development, exploration, and visualization in PhysiCell Studio (Heiland et al., 2024).

Citations for PhysiBoSS

If you used the PhysiBoSS extension to integrate Boolean networks into PhysiCell, please cite the most recent PhysiBoSS method paper in addition to PhysiCell:

Ponce-de-Leon, M., Montagud, A., Noël, V. et al. PhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks. npj Syst Biol Appl 9: 54 (2023). doi: 10.1038/s41540-023-00314-4

Suggestion

We suggest you refine the basic citation to reference PhysiBoSS, such as:

We used PhysiCell Version 1.14.1 (Ghaffarizadeh et al., 2018) with the PhysiBoSS extension for Boolean networks (Ponce-de-Leon et al., 2023) to build an agent-based simulation model.

Citations for PhysiMeSS

If you used the PhysiMeSS extension to model ECM fibers in PhysiCell, please cite the PhysiMeSS method paper in addition to PhysiCell:

Vincent Noël, Marco Ruscone, Robyn Shuttleworth, and Cicely K. Macnamara, PhysiMeSS - a new physiCell addon for extracellular matrix modelling, Gigabyte (2024). doi: 10.46471/gigabyte.136

Suggestion

We suggest you add a sentence just after citing PHysiCell, such as:

We used PhysiCell Version 1.14.1 to build an agent-based simulation model (Ghaffarizadeh et al., 2018). We also modeled ECM fibers using the PhysiMeSS extension (Noë et al., 2024).