Interactive Two-Part Virtual Miniworkshop on Open-Source CompuCell3D Multiscale, Virtual-Tissue Spatio-Temporal Simulations of COVID-19 Infection, Viral Spread and Immune Response and Treatment Regimes

How to Run, Extend, Adapt and Improve the CompuCell3D COVID-19 Model

Part I: Will be presented twice:

• First Presentation June 11th, 2020, 2PM-5PM EST (6 PM- 9PM GMT)

• Second Presentation June 12th (9AM - 12 noon EST (1 PM - 4 PM GMT)

Part II: Will be presented twice:

• First Presentation June 18th, 2020, 2PM-5PM EST (6 PM- 9PM GMT)

• Second Presentation June 19th (9AM - 12 noon EST (1 PM - 4 PM GMT)

Zoom Link for All Workshop Sessions https://iu.zoom.us/j/92556442274

Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding differences in disease outcomes and optimizing therapeutic interventions. In this two-part mini-workshop we present an open-source Python and CC3DML-scripted multiscale model and simulation of an epithelial tissue infected by a virus, a simplified cellular immune response and viral and immune-induced tissue damage and show how you can use it to model basic patterns of infection dynamics and antiviral treatment.

Part I presents the model and teaches how to run it and to change model parameters for generating new biologically meaningful simulations.

Part II teaches how to extend the model with additional images, graphics and file outputs, additional cell types, diffusive fields, cell behaviors and interactions and improved subcellular and immune-system models.

Audience: Anyone from undergraduates to faculty interested in COVID Modeling. Accessible to MDs, biologists, virologists, immunologists, drug developers, biochemists, biophysicists, mathematical and computational biologists. Background: For Part I--No programming or mathematics required. For Part II--Some experience with basic Python programming helpful, but not required--needed concepts will be covered in the workshop.

Learning Outcomes: At the end of Part I you will be able to download, modify and execute locally the base model structure, change all meaningful model parameters to simulate different immune states and drug treatments. At the end of part II you will be able to extend the model to include and analyze additional biological components and mechanisms.

For more information: see https://www.compucell3d.org or contact tjsego@gmail.com, or jaglazier@gmail.com

Instructors: Lead instructor: Dr. T.J. Sego, Associate instructors: Dr. James A. Glazier, Josua Aponte-Serrano, Juliano Gianlupi-Ferrari, and Dr. Gilberto Thomas.

After Workshop Support: We will be happy to help people develop their applications after the workshop and to collaborate on model development.

Computer Requirements: Any Windows or Mac computer. CompuCell3D also runs on many LINUX deployments (see www.compucell3d.org for details).

References:

• The current model description is available at https://www.biorxiv.org/content/10.1101/2020.04.27.064139v3

• CompuCell3D can be downloaded from https://compucell3d.org/SrcBin

• The source code for the COVID-19 model can be downloaded from Github at https://github.com/covid-tissue-models/covid-tissue-response-models

• and Google Drive at https://drive.google.com/drive/folders/1TcBnwa0wpbuXW58fQWwttWZWlzaMBD8P?usp=sharing

Before the first section: While we will cover CC3D installation in the Workshop, it will be helpful if you can download and install CC3D (from here) on your local computer or open a nanoHUB account and load the CC3D application in your workspace. It may be useful if you briefly review the basics of CC3D model specification, though these will be covered in the workshop.