Non-SOT Event: 19th Annual Multicell Virtual-Tissue Modeling Online Summer School

Starts:  Jul 28, 2024 09:00 AM (ET)
Ends:  Aug 4, 2024 05:00 PM (ET)

The Indiana University Biocomplexity Institute is pleased to announce the 19th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- 2024, which will take place between Sunday, July 28th and Sunday August 4th, 2024. We would very much appreciate your help in letting your colleagues and students know about this opportunity. 

This year’s workshop will take place over one seven-day week. The workshop will focus on the basics of building virtual tissue models modeling using CompuCell3D, as well as exploration of more advanced modeling topics using the many features and capabilities of the CompuCell3D software. A two-day model-building Hackathon in which attendees work in teams to build a functioning model of their problem of interest will be hosted on the weekend following the workshop (August 9–11). For first-time participants, attendance in the workshop is required for participation in the Hackathon. Previous workshop attendees or returning hackathon participants may contact us directly for admission into only the hackathon.

Summer school attendance guarantees admission to the Model-Building Hackathon. The Hackathon will group attendees by topic of interest. Experienced modelers will be embedded within each group. Workshop instructors will be available to assist Hackathon participants throughout the two-day session. Everyone will leave with a functioning core model that they can further customize, or even potentially develop into a publication! 

For more information, please see our announcements at

To register, please visit: More information on CompuCell3D is available at

Try out some example models online at NanoHub:

AUDIENCE: Mathematical Biologists, Computational Biologists, Experimental Biologists, Medical Scientists, Bioengineers, and Biophysicists, ranging from undergraduates to senior faculty, with a current or potential interest in mechanistic modeling of biological systems. The course covers multicellular modeling, which applies to developmental and tissue biology, tissue engineering, developmental diseases like cancer, in-host modeling of infection and immune response, and tissue-level toxicology. No specific programming or mathematical experience is required.


An Introductory Python and Principles of Modeling Tutorial will take place on July 28th, 2024. If you already know Python or have modeling experience, you may skip this tutorial (or take it as a review).

Multicell Virtual-Tissue Modeling Summer School: Basic Course (July 29th – August 4th, 2024) 

Mechanistic agent-based modeling is an integral part of contemporary bioscience, used for hypothesis generation and testing, experiment design and interpretation, and the design of therapeutic interventions. The CompuCell3D modeling environment allows researchers to rapidly build and execute complex Virtual Tissue simulations with minimal programming experience. CompuCell3D enables biological simulations from subcellular to tissue scales, supporting explicit cell shapes, cell migration, contact-mediated cell interactions, soluble signals, and complex cell state dynamics (gene regulatory, signaling, and metabolic networks). By the end of the course, participants will have had practice in using all the standard features of CompuCell3D needed to run a variety of multicellular simulations. Post-course support and collaboration will be available to continue simulation development of your biological problem(s) of interest.

Multicell Model-Building Hackathon (August 9th - August 11th, 2024):

By the end of the workshop, participants will have implemented a variety of simulations using many advanced features of CompuCell3D, including biochemical network modeling with CC3D, cell compartments and links, tissue folding, collective migration, and cell shape manipulation. Participants in the Hackathon will spend two days implementing a simulation of their biological problem of interest with support from the instructional team. Post-course support and collaboration will be available to continue simulation development.


  • Principles of modeling biological and biomedical problems
  • Python and Antimony scripting
  • Multicellular Virtual-Tissue simulations with CompuCell3D
  • Combining network models with virtual-tissue models in multiscale models


Prof. James A. Glazier (Indiana University), Prof. T.J. Sego (University of Florida, CompuCell3D lead developer), Dr. James Sluka (Indiana University), Prof. Julio Belmonte (North Carolina State University), Prof. Gilberto Thomas (Federal University of Rio Grande do Sul, Brazil), Pedro Cenci Dal Castel (Federal University of Rio Grande do Sul, Brazil), Dr. Priyom Adhyapok (Duke), Dr. Maciek Swat (CompuCell3D lead developer), Dr. Lorenzo Veschini (King’s College London).


Because the number of attendees is limited, admission is by application only. To apply for admission, please visit the school website at and to register, please visit:


June 1st, 2023. Applications will be processed as received. 
The workshop is partially supported by grants from the US National Institutes of Health. Enrollment is free.

We look forward to welcoming you online this August!


James A. Glazier
Biocomplexity Institute
Department of Intelligent Systems Engineering
Indiana University, Bloomington

James P. Sluka
Biocomplexity Institute
Department of Intelligent Systems Engineering
Indiana University, Bloomington


Online Instructions: