We are pleased to share the announcement of the 2023 Multicell Virtual-Tissue Modeling Online Summer School and Hackathon, which will take place at Indiana University Bloomington from July 31 through August 13, 2023.

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 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.

Physicists, biologists, computer scientists, and modelers team up to build research-grade models of biological systems. All experience levels are welcome.

Because the number of places is limited, admission is by application only. For more information, email compucell3d.iu@gmail.com or visit www.compucell3d.org/Workshop23. Register at: www.tinyurl.com/CC3D2023.

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.

AIM AND FOCUS:

An Introductory Python and Principles of Modeling Tutorial will take place on July 31st:

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: 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.

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), 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). 

PARTICIPATION:

Because the number of places is limited, admission is by application only. To apply for admission, please visit the school website www.compucell3d.org/Workshop23, and to register please visit: www.tinyurl.com/CC3D2023.

DEADLINE for APPLICATIONS:

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.

Email: compucell3d.iu@gmail.com | URL: compucell3d.org | Apply: www.tinyurl.com/CC3D2022