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

We rapidly created and deployed a cloud-hosted model with an interactive Web-based graphical user interface (GUI) running on nanoHUB (nanohub.org) using xml2jupyter Version 1.1 109 . The web-hosted model can be run at https://nanohub.org/tools/pc4covid19. This workflow uses a Python script that converts a PhysiCell configuration file (in XML) into a Jupyter notebook and adds additional Python modules for the GUI. The automated process of converting a standalone PhysiCell model into an interactive Jupyter notebook version (a GUI) takes just a few minutes. The resulting GitHub repository is shared with the nanoHUB system administrators who install it for testing as an online, executable model (an "app"). After we perform usability and other testing and finalize documentation,, it is published and becomes available for public use. The whole process (including the initial development of the core PhysiCell model) took less than 12 hours for this particular app. See