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17th Annual Multicell Virtual-Tissue Modeling Online Summer School and Hackathon

  • 31 Jul 2022
  • 7 Aug 2022
  • Virtual
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. 

For more information, please see our announcement at https://compucell3d.org/Workshop22

To register, please visit: www.tinyurl.com/CC3D2022. More information on CompuCell3D is available at https://compucell3d.org/.

AUDIENCE: 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.


An Introductory Python and Principles of Modeling Tutorial will take place on 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 1nd - 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 (https://nanohub.org/tools/cc3dbase4x). 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. Lorenzo Veschini (King’s College London); Prof. Yi Jiang (Georgia State University); Dr. Priyom Adhyapok (Duke), Dr. Maciek Swat (CompuCell3D lead developer).


Because the number of places is limited, admission is by application only. To apply for admission, please visit the school website at https://compucell3d.org/Workshop22
and to register, please visit: www.tinyurl.com/CC3D2022. 


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!

James A. Glazier

Department of Intelligent Systems Engineering
Indiana University, Bloomington


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