physicell.github.io/Training.html at main · PhysiCell/physicell.github.io · GitHub

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    <title style="color:white;">PhysiCell Project Website: Training</title>
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        <h1 ID="top">Training and Documentation</h1>
        <!--
        <p>While this is under construction, I suggest visiting our
        <a href="https://github.com/physicell-training/institut-curie-2024">2024 PhysiCell Mini Course</a>.
        </p>
        -->

            <p>We divide PhysiCell's training curriculum into several <a href="#short_courses">short courses</a>:</p>
            <dl>
                <dt><a href="#essentials">Essentials</a>: </dt>
                <dd>A hands-on primer to introduce agent-based modeling and simulation with PhysiCell Studio.
                    All PhysiCell users and developers should start here.
                    No software installlation is required.
                </dd>

                <dt><a href="#PhysiBoSS">Boolean Networks with PhysiBoSS</a></dt>
                <dd>A hands-on introduction to adding Boolean networks to cell agents with PhysiBoSS in PhysiCell Studio.
                    PhysiCell and PhysiBoSS users should continue here only after completing <a href="#essentials">PhysiCell Essentials</a> training. Some C++ may be required.
                </dd>

                <dt><a href="advanced_modeling">Advanced PhysiCell Modeling</a></dt>
                <dd>Learn to develop custom model components and visualizations in C++. Learn to use C++ extensions for ODEs (via libRoadrunner), ECM fibers (via PhysiMeSS), and more.
                    PhysiCell and PhysiBoSS users and developers should complete
                    <a href="#essentials">Essentials</a> and <a href="#PhysiBoSS">PhysiBoSS</a> training first.
                    C++ (including a PhysiCell C++
                    developement environment) are required.
                </dd>

                <dt><a href="PhysiCell_developers">PhysiCell for Developers</a></dt>
                <dd>Learn about the PhysiCell core C++ structure and APIs, and how to contribute to C++ core and extensions.
                    PhysiCell and PhysiBoSS users and developers should complete
                    <a href="#essentials">Essentials</a>, <a href="#PhysiBoSS">PhysiBoSS</a>, and
                    <a href="#advanced_+modeling">Advanced Modeling</a> training first.
                    C++ (including a PhysiCell C++ developement environment) are required. </dd>
            </dl>

            <h2 ID="short_courses">Training Courses</h2>

            <h3 ID="essentials">PhysiCell Essentials</h3>
            <p>This short course is the place to start, whether new to modeling, planning serious models in PhysiCell, or preparing for more advanced C++ based customizations. We'll introduce agent-based modeling (and PhysiCell), and lead you through several hands-on exercises to create models, without need for coding. </p>
            <p>The work can be done in a web browser or in PhysiCell Studio, and no background coding (or deep knowledge of biology) is required.</p>

            <h4>Prerequisites</h4>
            <ul>
                <li><b>Background knowledge:</b> Basic knowledge of biology, and concepts of mathematical functions.</li>
                <li><b>Software setup:</b> Web browser, or optional PhysiCell Studio Desktop</li>
            </ul>

            <h4>Sessions</h4>

            <h5>Session 1: Introduction to Agent-Based Modeling and PhysiCell </h5>

            <ul>
                <li><b>Slides:</b> <a href="https://github.com/physicell-training/essentials/blob/main/slides/Introduction_to_ABM_and_PhysiCell_(v2025.10.18).pdf?raw=true">Click Here</a> </li>
                <li><b>Recording:</b> </li>
            </ul>

            <h5 style="font-style:italic; font-color: grey;">Optional: Desktop Installation of PhysiCell Studio</h5>

            <ul>
                <li><b>Slides:</b> (in development)</li>
                <li><b>Recording:</b> </li>
            </ul>


            <h5>Session 2: Hands-on work Part 1: Getting Started, and Villager/Zombie Model</h5>

            <ul>
                <li><b>Slides:</b> <a href="https://github.com/physicell-training/essentials/blob/main/slides/PhysiCell_introduction_hands_on_part_1_(v2025.02.16).pdf?raw=true">Click here</a> </li>
                <li><b>Code:</b> <a href="https://github.com/physicell-training/essentials/blob/main/code/zombies_and_villagers.zip?raw=true">Zombies &amp; Villagers example</a> (unzip in <span class="code">user_projects</span>)</li>
                <li><b>Recording:</b> </li>

            </ul>

            <h5>Session 3: Hands-on work Part 2: Cancer Chemotherapy & Immunology Models</h5>

            <ul>
                <li><b>Slides:</b> <a href="https://github.com/physicell-training/essentials/blob/main/slides/PhysiCell_introduction_hands_on_part_2_(v2025.02.16).pdf?raw=true">Click here</a></li>
                <li><b>Code:</b> <a href="https://github.com/physicell-training/essentials/blob/main/code/basic_cancer_immune_drug.zip?raw=true">Cancer-immune example</a> (unzip in <span class="code">user_projects</span>)</li>

                <li><b>Recording:</b> </li>
            </ul>

            <h5 style="font-style:italic;">Optional: Notes and Tips on Parameter Estimates</h5>

            <ul>
                <li><b>Slides:</b> (in development)</li>
                <li><b>Recording:</b> </li>
            </ul>

            <p class="center">[ <a href="#top">return to top</a> ]</p>

            <h3 ID="PhysiBoSS">Integration of Boolean Networks with PhysiBoSS</h3>
            <p>
            This short course builds upon the <a href="#essentials">PhysiCell Essentials</a> training to introduce Boolean signaling models, and how to add them to cell agents using PhysiBoSS. Early readers can get started by reading the excellent guide in <a href="https://doi.org/10.1093/bib/bbae509">Ruscone et al. (2024)</a>.
            </p>
            <p class="center">[ <a href="#top">return to top</a> ]</p>

            <h3 ID="advanced_modeling">Advanced PhysiCell Modeling</h3>
            <p>This short course builds upon the training in <a href="#essentials">Essentials</a> and <a href="#PhysiBoSS">PhysiBoSS</a> to help users learn how to build custom code and visualization in C++. It also introduces C++ based extensions including libRoadrunner (for ODE models) and PhysiMeSS (for ECM fiber modeling). </p>

            <p>This course requires a working PhysiCell C++ development environment.</p>
            <p class="center">[ <a href="#top">return to top</a> ]</p>

            <h3 ID="physicell_developers">PhysiCell for Developers</h3>
            <p>This short course further builds off of the <a href="#advanced_modeling">Advanced Modeling</a> training to introduce PhysiCell's core C++ structure, with a focus on how to contribute to the core C++ libraries, as well as community extensions. </p>

            <p>This course requires a working PhysiCell C++ development environment.</p>
            <p class="center">[ <a href="#top">return to top</a> ]</p>


        <h2>Other Guides</h2>
        <p></p>
        <p class="center">[ <a href="#top">return to top</a> ]</p>

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