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

(1) Open source and GitHub: All simulation source code is shared as open source on GitHub, with welldefined, versioned and documented releases, and Zenodo-generated DOIs and archives. (2) Interactive cloud-hosted models: Every prototype version is rapidly transformed into a cloud-hosted, interactive model to permit faster scientific communication across communities, particularly with virologists and others who have essential insights but ordinarily would not directly run the simulation models. (3) Social media and virtual feedback: We enlist community participation (feedback, modeling contributions, software contributions, and data contributions) through social media, virtual seminars, web-based forms, and a dedicated Slack workspace. We are particularly encouraging feedback and data contributions by domain experts in virology, epidemiology, and mathematical biology (with a focus (4) Frequent preprint updates: Each model iteration is accompanied by a cloud-hosted, interactive app (see #2) and an updated preprint on bioRxiv. (5) Integration of feedback: All community feedback is evaluated to plan the next set of model refinements and recorded in an updated bioRxiv preprint.