Announcing the 17th Annual CompuCell3D Virtual Tissues Workshop and Hackathon

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Hayden Fennell

May 10, 2022, 5:06:48 PM5/10/22
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Please forward this announcement to anyone that you think might be interested.

We are pleased to announce the 17th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- 2022, which will take place between Sunday July 31st and Sunday August 8th, 2022 at Indiana University, Bloomington.

For more information, please see the attached flyer or our announcement at

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


Mathematical Biologists, Computational Biologists, Experimental Biologists, Medical Scientists and Biophysicists, 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.

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. Everyone will leave with a functioning core model that they can further customize. Advanced modelers can apply to attend just the Hackathon. 


Introductory Python and Principles of Modeling Tutorial (July 31st, 2022):

If you already know Python or have modeling experience, you may skip this Tutorial or take this material as a review

Multicell Virtual-Tissue Modeling Summer School (August 1st - August 5th, 2022) and Hackathon (August 6th - August 7th, 2022):

Mechanistic 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 with modest programming experience to rapidly build and execute complex Virtual Tissue simulations of development, homeostasis, toxicity and disease in tissues, organs and organisms, covering sub-cellular, multi-cell and continuum tissue scales. Virtual-Tissue simulations developed using CompuCell3D run on Windows, Mac and Linux and online via the nanoHUB CompuCell3D deployment ( CompuCell3D is open source, allowing users to extend, improve, validate, modify and share the core software. By the end of the Summer School and Hackathon, participants will have implemented a basic simulation of their particular biological problem of interest. Post-course support and collaboration will be available to continue simulation development.


The summer school will include five days of lectures and hands-on computer tutorials. In the modeling Hackathon teams of advanced and beginner modelers will develop research-quality models of their systems of interest. Each attendee will also present a mini talk on their problem of interest. We will provide after-hackathon support to assist users in the development of these models in their research.


  • 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), Dr. T.J. Sego (Indiana University, CompuCell3D lead developer), Dr. James Sluka (Indiana University), Prof. Julio Belmonte (North Carolina State University), Dr. Josua Aponte Serrano (NIAID), 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)


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


June 1st, 2022. 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!

Hayden Fennell 
On behalf of Dr. James Glazier (jaglazier [at]
Department of Intelligent Systems Engineering
Indiana University, Bloomington
haydenfennell [at]
2022CC3D Workshop Flyer.pdf
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