We are pleased to announce the Online 20th Annual CompuCell3D Multicell Virtual Tissue Modeling Workshop and Hackathon -- 2025,which will take place between Monday July 28th and Sunday August 10th, 2025. 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.

Workshop 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 athttps://compucell3d.org/Workshop25

To register, please visit: https://tinyurl.com/CC3D2025. More information on CompuCell3D is available at https://compucell3d.org/. The workshop is partially supported by grants from the US National Institutes of Health.

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

AGENDA:

Introductory Python Tutorial Course (July 19th, 2025)

CompuCell3D code is written primarily in Python code. A small amount of Python knowledge is needed to write custom model code in CompuCell3D. We provide an introductory Python course in advance of the workshop to teach you everything that you will need to know to use CompuCell3D during the workshop. If you already know Python or have modeling experience, you may skip this tutorial or take it as a review.

Multicell Virtual-Tissue Modeling Course: Basic Course (July 28th - August 1st, 2025) 

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 Course: Advanced Topics (August 4th - August 6th, 2025)

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 cell compartments and epithelia, cell links and focal point plasticity, tissue folding, and best practices for parameterization and data handling, among other topics. 

Model-Building Hackathon (August 8th – August 10th, 2025)

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. Participation in at least one week of the workshop guarantees entry to the hackathon. If you have previously attended our training workshop or already have experience with CompuCell3D and would like to attend only the hackathon, please feel free to contact us to set up a hackathon-only registration. 

CORE TOPICS: 

• 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

INSTRUCTORS:

Prof. James A. Glazier (Indiana University), 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 (Indiana University), Hayden Fennell (Indiana University), Dr. Priyom Adhyapok (Duke University), Prof. T.J. Sego (University of Florida, CompuCell3D lead developer), Dr. Maciek Swat (CompuCell3D lead developer).

PARTICIPATION:

Because the number of attendees is limited, admission is by application only. To apply for admission, please visit the workshop website at https://compucell3d.org/Workshop25

and to register, please visit: www.tinyurl.com/CC3D2025.  

A $25.00 USD non-refundable application fee will be charged upon application to the workshop. Enrollment is confirmed once application is accepted and fee has been paid. Please read the application instructions on the registration page carefully for details about the payment process.

We recognize that international exchanges rates and other circumstances may make the application fee prohibitive for some applicants. If you would like to apply for a fee waiver for any reason, please contact our coordinator, Hayden Fennell (hfennel@iu.edu), for more details.

Deadline for applications is June 1st, 2025. Applications will be processed as received. 

We look forward to welcoming you online this August!

James A. Glazier

Department of Intelligent Systems Engineering

Indiana University, Bloomington

jaglazier@gmail.com