Open Virtual Tissues (OpenVT)

The OpenVT project is at openvt.org.

Background

OpenVT seeks to build an engaged community of researchers - modelers and software engineers who use and develop open source multicellular modeling frameworks. These frameworks allow virtual experiments (simulations) of cell behaviors within tissues and organs. The goals of OpenVT are to:

• educate the community of modelers on the features that each framework offers, via
  • a living spreadsheet with features of each framework
  • links to documentation and tutorials
  • publications that used a framework to build a model or highlight functionality
  • reference models to compare simulation results from different frameworks
• provide easier model sharing between frameworks
• provide steps toward model reproducibility between frameworks
• share ideas or functionality between frameworks
• seek new funding opportunities related to this overall project

Papers comparing frameworks

Some relevant publications that have compared multicellular modeling frameworks include:

• Comparing individual-based approaches to modelling the self-organization of multicellular tissues (2017). James M. Osborne, Alexander G. Fletcher, Joe M. Pitt-Francis, Philip K. Maini, David J. Gavaghan. https://doi.org/10.1371/journal.pcbi.1005387

• A Review of Cell-Based Computational Modeling in Cancer Biology (2019). John Metzcar, Yafei Wang, Randy Heiland, Paul Macklin. https://doi.org/10.1200/CCI.18.00069

• Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization (2020). Rafael R. Bravo, Etienne Baratchart, Jeffrey West, Ryan O. Schenck, Anna K. Miller, Jill Gallaher, Chandler D. Gatenbee, David Basanta, Mark Robertson-Tessi, Alexander R. A. Anderson. https://doi.org/10.1371/journal.pcbi.1007635

Frameworks and their features

One goal of the OpenVT project is to provide text-based schemas that the community can fill in and maintain that describe features of each modeling framework. These schemas are accessible on GitHub and updating them will follow the usual GitHub workflow using Pull Requests (PRs). If you are taking some responsibility for providing/updating a framework's features and are unfamiliar with GitHub PRs, please contact us for assistance.

• Current list of frameworks
• Schema details
• Interactive search of features - Prototype Demo only!

Reference Models

• Persistent Random Walk / Biased Motility
• Monolayer growth
• Wound healing without migration
• Chemotaxis across the domain; one cell
• Cell sorting
• Angiogenesis

Presentations and Workshops

• Simulating tissue dynamics with cellular Potts models
• NSF I-Corps: Jan-Feb 2024 (virtual training for POSE Awardees)
• "Computational Modeling in Biology" Network (COMBINE) - Harmony workshop - April 8, 2024
• IMAG Multiscale Modeling and Viral Pandemics WG - May 2, 2024
• SMB 2024 - OpenVT workshop

Funding

National Science Foundation (Award 2303695)