PhysiCell Studio: a graphical tool to create, execute, and visualize a multicellular model

Randy Heiland

Indiana University

"PhysiCell Studio: a graphical tool to create, execute, and visualize a multicellular model"

Defining a multicellular model can be challenging. There may be hundreds of parameters that specify the attributes and behaviors of multiple cell types and diffusible substrates in a model. If the model can be defined using a format specification, e.g., a markup language, then it can be readily shared in a minimal first step towards reproducibility. However, specifying the parameters of cell behaviors and substrates by hand is time consuming, error-prone, and ultimately a limiting factor in rapidly developing and refining sophisticated multicellular models. PhysiCell is an open source physics-based multicellular simulation system with an active and growing user community. It uses XML (extensible markup language) to define a model. To date, users needed to manually edit the XML to modify a model. PhysiCell Studio is a graphical tool to simplify this task. It provides a multi-tabbed GUI (graphical user interface) that allows graphical editing of the model and its associated XML, including the creation/deletion of fundamental objects, e.g., cell types and substrates/signals in the microenvironment. It also lets users run their model and interactively visualize results, allowing for more rapid model refinement. Using PhysiCell Studio in the classroom and training workshops has significantly reduced the training time for new learners, allowing them to develop sophisticated modeling. Conversely, frequent classroom and workshop use of the Studio has driven substantial improvements to the GUI. Like PhysiCell, the Studio is open source software, and contributions from the community are encouraged.
Additional authors: Vincent Noël (Institut Curie), Paul Macklin (Indiana University)

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