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    <title style="color:white;">PhysiCell Project: Citing PhysiCell</title>
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       <h1>Citing PhysiCell</h1>

        <a name="basic_citation"></a>
        <h2>PhysiCell method citation</h2>

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

       <p class="quote">
        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: <a href="https://dx.doi.org/10.1371/journal.pcbi.1005991">10.1371/journal.pcbi.1005991</a>.
        </p>

        <h3>Suggestion</h3>
        <p>Suppose you used PhysiCell Version 1.14.1 in your work. We suggest a sentence like this in your Method section:</p>

        <p class="quote">
            We used PhysiCell Version 1.14.1 to build an agent-based simulation model (Ghaffarizadeh et al., 2018).
        </p>

        <h2>Basic PhysiCell method description</h2>
        <p>For writing your method section, you may want a basic description of the PhysiCell framework. Please consider
            quoting a brief description we have used. </p>


            <p class="quote">
        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)."</p>

        <p>This description references:</p>

        <ul>
            <li>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: <a href="https://doi.org/10.1038/s41540-024-00472-z">10.1038/s41540-024-00472-z</a>.
            </li>

            <li>A. Ghaffarizadeh et al., BioFVM: an efficient, parallelized diffusive transport
                solver for 3-D biological simulations, Bioinformatics 32(8): 1256-8 (2016).
                doi: <a href="https://doi.org/10.1093/bioinformatics/btv730">10.1093/bioinformatics/btv730</a>.
            </li>

            <li>J. Ozik et al., P. Learning-accelerated discovery of immune-tumour interactions.
            Mol. Syst. Des. Eng. 4: 747-760 (2019). doi: <a href="https://dx.doi.org/10.1039/C9ME00036D">10.1039/C9ME00036D</a>
            </li>

            <li>M. Getz et al., Iterative community-driven development of a sars-cov-2 tissue simulator,
                bioRxiv 2020.04.02.019075 (2021); doi: <a href="https://doi.org/10.1101/2020.04.02.019075">10.1101/2020.04.02.019075</a>
                </li>

            <li>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: <a href="https://dx.doi.org/10.1016/j.isci.2021.102935">10.1016/j.isci.2021.102935</a>.
            </li>

            <li>Y. Wang et al., Impact of tumor-parenchyma biomechanics on liver metastatic progression:
                a multi-model approach. Sci. Rep. 11: 1-20 (2021). doi:
                <a href="htts://dx.doi.org/10.1038/s41598-020-78780-7">10.1038/s41598-020-78780-7</a>
            </li>

            <li>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:
                <a href="https://dx.doi.org/10.1016/j.isci.2022.104395">10.1016/j.isci.2022.104395</a>.
            </li>


        </ul>

        <h2>Adding citations of PhysiCell extensions</h2>

        <h3>Citations for PhysiCell rules / grammar</h3>
        <p>If you used the modeling grammar / language to construct your simulation model, please cite
            its recent preprint in addition to PhysiCell:         </p>

        <p class="quote">J.A.I. Johnson et al., Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.
        bioRxiv 2023.09.17.557982 (2024); doi: <a href="https://doi.org/10.1101/2023.09.17.557982">10.1101/2023.09.17.557982</a>.
        </p>

        <h4>Suggestion</h4>
        <p>We suggest you add a sentence just after <a href="basic_citation">citing PHysiCell</a>, such as:</p>

        <p class="quote">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.).</p>

        <h3>Citations for PhysiCell Studio (including PhysiCell Cloud)</h3>
        <p>If you used PhysiCell Studio to build, explore, and/or visualize your model, please cite its method paper in addition to
            PhysiCell: </p>


        <p class="quote">
            Randy Heiland, Daniel Bergman, Blair Lyons, Grant Waldow, Julie Cass,
            Heber Lima da Rocha, Marco Ruscone, Vincent No&euml;l, and Paul Macklin,
            PhysiCell Studio: a graphical tool to make agent-based modeling more accessible.
            Gigabyte, 2024. doi: <a href="https://doi.org/10.46471/gigabyte.128">10.46471/gigabyte.128</a>.
        </p>

        <h4>Suggestion</h4>
        We suggest you refine the <a href="#basic_citation">basic citation</a> to reference PhysiCell Studio, such as:

    <p class="quote">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).
    </p>


        <h3>Citations for PhysiBoSS</h3>
        <p>If you used the PhysiBoSS extension to integrate Boolean networks into PhysiCell, please  cite the
            most recent PhysiBoSS method paper in addition to PhysiCell: </p>

            <p class="quote">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: <a href="https://doi.org/10.1038/s41540-023-00314-4">10.1038/s41540-023-00314-4</a>
            </p>

            <h4>Suggestion</h4>
            <p>We suggest you refine the <a href="basic_citation">basic citation</a> to reference PhysiBoSS, such as:</p>

        <p class="quote">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.</p>

        <h3>Citations for PhysiMeSS</h3>
        <p>If you used the PhysiMeSS extension to model ECM fibers in PhysiCell, please cite the
            PhysiMeSS method paper in addition to PhysiCell: </p>

            <p class="quote">Vincent No&euml;l, Marco Ruscone, Robyn Shuttleworth, and Cicely K. Macnamara,
                PhysiMeSS - a new physiCell addon for extracellular matrix modelling,
                Gigabyte (2024). doi: <a href="https://doi.org/10.46471/gigabyte.136">10.46471/gigabyte.136</a>
            </p>

            <h4>Suggestion</h4>
            <p>We suggest you add a sentence just after <a href="basic_citation">citing PHysiCell</a>, such as:</p>

            <p class="quote">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 (No&euml; et al., 2024).</p>


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