openvt.github.io

Open Virtual Tissues (OpenVT)

Background

OpenVT seeks to build an engaged community of researchers that 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 users on the features that each framework offers, via
  • comparative spreadsheets of capabilities
  • links to documentation
  • publications that highlight the frameworks (either specific models or general information)
  • reference models to compare simulation results from frameworks
• provide easier model sharing between frameworks
• provide steps toward model reproducibility between frameworks
• seek new funding opportunities related to this overall project

Articles 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

Funding

National Science Foundation (Award 2303695)