18th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- Indiana University, Bloomington, Indiana, USA, July 31st to August 13th, 2023

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CC3D 2023 Class Brochure

We are pleased to announce the 18th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon -- 2023, which will take place between Monday July 31st and Sunday August 13th, 2023. We would very much appreciate your help in letting your colleagues and students know about this opportunity. A flyer announcing the workshop is attached.

This year’s workshop will take place over the course of two weeks. The first week will focus on the basics of building virtual tissue models modeling using CompuCell3D. The second week will focus on advanced modeling topics, as well as advanced 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 at the end of the advanced course. Attendees are welcome to attend only the first week, only the second week, or both weeks of the course. Attendance in the first week is not required to attend the advanced portion of the course. Attendance of at least one week of the workshop is required for participation in 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.

For more information, please see our announcements at https://compucell3d.org/Workshop23

To register, please visit: https://tinyurl.com/CC3D2023. More information on CompuCell3D is available at https://compucell3d.org/.

Try out some example models online at NanoHub: https://compucell3d.org/Models-nanoHub.


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 31st, 2023. 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 (August 1st - August 4th, 2023)

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 Virtual-Tissue Modeling Summer School: Advanced Topics and Hackathon (August 7th - August 13th, 2023):

By the end of the Advanced Topics course, participants will have implemented a variety of simulations using advanced features of CompuCell3D. The advanced course will include instruction on biochemical network modeling with CC3D, cell compartments and epithelia, and CC3D extension development. CompuCell3D natively supports SBML, Antimony, and MaBoSS network model integration. 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 University), Dr. Josua Aponte-Serrano (National Institute of Allergy and Infectious Diseases.


Because the number of places is limited, admission is by application only. To learn more about the workshop, please visit the school website at https://compucell3d.org/Workshop23. Details will be updated regularly as the course approaches. To apply for admission, please visit: www.tinyurl.com/CC3D2023. Application is free. 


June 1st, 2023. Applications will be processed as received.


For any questions or concerns about the workshop, or if you encounter any issues during registration, please contact Hayden Fennell at hfennel@iu.edu.

This workshop is partially supported by grants from the US National Institutes of Health. Enrollment and attendance are free. 

We look forward to welcoming you online this August!

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

2023 CC3D Clas FlierCC3D 2023 Class Brochure

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