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bioRxiv · 10.1101/2023.10.24.563727

PhysiCell Studio: a graphical tool to make agent-based modeling more accessible

Heiland, R.·Bergman, D. R.·Lyons, B.·Cass, J.·L. Rocha, H.·Ruscone, M.·Noël, V.·Macklin, P.
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Abstract

Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of objects. Hopefully the model will be defined using some format specification, e.g., a markup language, that will provide easy model sharing (and a minimal step toward reproducibility). PhysiCell is an open source, physics-based multicellular simulation framework with an active and growing user community. It uses XML to define a model and, traditionally, users needed to manually edit the XML to modify the model. PhysiCell Studio is a tool to make this task easier. It provides a graphical user interface that allows editing the XML model definition, including the creation and deletion of fundamental objects, e.g., cell types and substrates in the microenvironment. It also lets users build their model by defining initial conditions and biological rules, run simulations, and view results interactively. PhysiCell Studio has evolved over multiple workshops and academic courses in recent years which has led to many improvements. Its design and development has benefited from an active undergraduate and graduate research program. Like PhysiCell, the Studio is open source software and contributions from the community are encouraged.

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Heiland, R., Bergman, D. R., Lyons, B., Cass, J., L. Rocha, H., Ruscone, M., Noël, V., Macklin, P.. 2023-10-27. PhysiCell Studio: a graphical tool to make agent-based modeling more accessible. https://doi.org/10.1101/2023.10.24.563727

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