Rapid community-driven development of a SARS-CoV-2 tissue simulator

Yafei Wang; Randy Heiland; Morgan Craig; Courtney L. Davis; Ashlee N Ford Versypt; Adrianne Jenner; Jonathan Ozik; Nicholson Collier; Chase Cockrell; Andrew Becker; Gary An; James A. Glazier; Aarthi Narayanan; Amber M Smith; Paul Macklin

To facilitate rapid cloud-hosted dissemination of PhysiCell-powered models on the nanoHUB platform, we developed xml2jupyter to automatically generate a Jupyter-based graphical user interface (GUI) for any PhysiCell model 109 . The Jupyter notebook includes widgets to set parameters, initiate a simulation run, and visualize diffusing substrates and cell agents. In turn, we also developed a protocol to deploy the PhysiCell model and the Jupyter notebook interface on nanoHUB as a cloud-hosted, interactive model. This allows developers to rapidly convert a locally executable, command-line model to a cloud-hosted shared model with graphical interface in a matter of minutes to hours (depending upon testing speed on nanoHUB).