Announcing the 2025 OpenVT Multicellular Modelling Workshop at the Annual Society of Mathematical Biology (SMB) meeting

We are pleased to announce the 2025 OpenVT Workshop on Multiscale Model Sharing and Reproducibility, being held as a satellite meeting of the Society of Mathematical Biology (SMB) meeting, on July 13th 2025 at the University of Alberta, Edmonton, Alberta Canada. Building complex multicellular agent-based biological simulations (virtual tissues) in a sharable, extensible and reproducible way is challenging but critical to advancing research and enhancing deployment.

This one day, two part (AM/PM) workshop will offer tutorials on using popular multicellular modelling frameworks which support rapid simulation construction and distribution and a multicellular model reproducibility hackathon which will explore best practice for model design and distribution.

  • Part 1: Multicellular Model Development Tutorials
  • Part 2: Multicellular Modelling Hackathon/Reproducibility Challenge
  • To Register: sign up here

    • Community Development of Multicellular Virtual Tissues: The OpenVT project

    Abstract

    Multicellular simulations have become indispensable in understanding complex biological phenomena, from tissue development to disease progression. But the diversity in simulation methods - from agent-based models, cellular Potts models, cellular automata, lattice-free models, stochastic particle simulations, etc - poses challenges in reproducibility, modularity, reusability, and integration within multi-scale simulation. This workshop aims to bridge these gaps by focusing on the development of standards and schemas, with special emphasis on multiscale, embedded, and coupled simulation methods. Through short presentations and discussion, attendees will see the need for standardization, and the importance of sharing and reusing models.

    Time

    Sunday July 13th, 2025 9:30am-5:00pm Mountain Daylight Time (MDT)

    Venue

    Aurora Room in Lister Centre at the University of Alberta

    Note we will be heading out for Lunch at the student union building and there is a coffee shop nearby for refreshments.

    Schedule for Workshop

    9:30am - 12:30pm Part 1: Multicellular Model Development Tutorials

    Timeframe Description
    9:00am-9:30am Arrive and setup.
    9:30am-9:50am Welcome and admin (20 min)
    9:50am-10:30am 5 min intro from tools. (6 tools 40 minutes)
    10:30am-12:30pm Split for individual tutorials (2 hours with 15 minutes break)
    Name Description Website
    Chaste Chaste (Cancer, Heart and Soft Tissue Environment) is a general-purpose simulation package aimed at simulating biological systems, particularly focusing on cardiac, cancer, and soft tissue modeling. link
    CompuCell3D A flexible and extensible simulation environment for multi-cellular systems biology, including the use of cellular Potts models. link
    Morpheus A modeling and simulation environment for the study of multi-scale and multicellular systems, able to couple ODEs, PDEs and cellular Potts models. link
    PhysiCell A physics-based cell simulator that models 3D multicellular systems, focusing on the interactions of (off-lattice) cells with their microenvironment. link
    Tissue Forge Tissue Forge is an interactive, particle-based physics, chemistry and biology modeling and simulation environment. link
    Vivarium The Vivarium Collective is a registry for open-source Vivarium-compatible simulation modules. These can be wired together to generate novel multi-scale simulations, with the most appropriate algorithm for each biological mechanism. link

    1:30pm - 5:00pm Part 2: Multicellular Modelling Hackathon/Reproducibility Challenge

    Timeframe Description
    1:30pm-2:00pm

    Introduction and specification of challenge model problem (30 min)
    2:00pm-4:30pm 2:00-4:30 Hackathon working on implementing challenge model problem (2.5 hours with 15 min break)
    4:30pm-5:00pm Presenting results of hackathon (30 min)

    Preparation

    Before the workshop we recommend you check the prerequisites and complete the preparation tasks for the tools you intend to use on the day (including to participate in the tutorials).

    Name Lead(s) email Description Website
    Chaste James Osborne The simplest way to run simulations in the Chaste framework is to use the docker setup as this works in all OSs (Linux MacOS and Windows). Before the workshop you will need to download and install docker, and download the chaste docker container (this contains the source code you will need).
    • Install Docker and allocate it at least 4GB RAM
    • On the command line run the following: docker run -it --init --rm -v chaste_data:/home/chaste chaste/release
    • This is your terminal on Chaste we will work in here in the workshop.
    • To make things easier you should also Install VSCode for editing code and Paraview for visualisation.
      • For more details see this documentation and this README file.
    		link
    CompuCell3D James Glazier and Joel Vanin This session will provide a hands-on introduction to using the open-source CompuCell3D modeling environment to construct and execute compact and sharable multiscale, multicellular Virtual-Tissue models for developmental, cancer, toxicology, and infectious-disease applications. Members of the audience will build and explore how CompuCell3D can simplify the construction of complex, extensible and reusable Virtual Tissue models. Key topics will include: installing and running CompuCell3D, principles of CompuCell3D Physics, representation of cell behaviors and interactions as effective energies and constraints, CC3DML and Python model-specification basics, and representing complex network models in CompuCell3D. Several hands-on exercises will be incorporated to provide practice with the software.
    • CompuCell3d models will be run locally on your machine.
    • Binaries can be found on the website: please download and install in advance - and test one of the Demo models.
    • There is a one-button installer for Windows machines, but be sure to install to a local directory (not a ONE-drive directory) where you have write privileges. Installation takes some time; but if it fails to complete, please run the installer again (do not delete and reload).
    • Installation on Macs and Linux systems depends on the chip set and operating systems details, so please follow the instructions carefully. If you have difficulty installing CompuCell3D, please contact jaglazier@gmail.com and we will try to arrange to help you.
    • For Installation on Macs with an M1-M3 processors (newer Macs) * CompuCell3D 4.6.0 - MacOS arm64 processors (M1, M2) Download the installer NOTE: the file cc3d-installer-osx-4.6.0-arm64.sh will automatically download and be put into your downloads folder unless you have previously designated a different folder for automatic downloads.
    • Run the following commands:
    • chmod +x cc3d-installer-osx-4.6.0-arm64.sh.
    • /cc3d-installer-osx-4.6.0-arm64.sh
    • For further help on utilizing CC3D to run your own models please see the documentation.
    • You can find slides, exercises and supporting materials for this miniworkshop: here
    • You can find our extensive course on using CompuCell3d: here
    		link
    Morpheus Simon Syga and Jupiter Algorta Morpheus will run locally on your laptop and quick installers are available for your OS (Windows, Linux, MacOS) from the homepage: here - so please download and install before the workshop and check with the GUI/Examples and GUI/File/Settings that your local gnuplot and ffmpeg are found and work with Morpheus.
    • Browse the model repository at here to get an overview of modeling capabilities
    • Or watch online courses, videos here.
    		 link
    PhysiCell Paul Macklin and Randy Heiland We plan to teach PhysiCell using the Web-based Galaxy platform.
    • See instructions for getting an account and running PhysiCell Studio here.
    • As a backup, also please register for an account on nanoHUB, in case we want to switch to the PhysiCell Studio app there.
    • For an introduction to agent-based modeling and PhysiCell, see website.
    		 link
    Tissue Forge TJ Sego For details see website link
    Vivarium Eran Agmon In this session, I will introduce Vivarium’s design principles and demonstrate Vivarium 2.0, also known as process bigraph, a next-generation engine for integrative multiscale simulation. Participants will learn how to build and connect processes, explore scalable model composition, and use emerging tools for collaborative, open-ended systems biology.
    • Vivarium 1.0 paper: here
    • Vivarium 1.0 Docs: here
    • Vivarium 1.0 GitHub: here
    • Vivarium 2.0 GitHub: here
    • Compositional Systems Biology preprint: here
    • Vivarium-based E. coli whole-cell model GitHub: here
    		 link