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Combined 2020 Network Modeling Summer School and Hackathon and Multicell Virtual-Tissue Modeling Summer School and Hackathon.

  • 26 Jul 2020
  • 9 Aug 2020

Combined 2020 Network Modeling Summer School and Hackathon and Multicell Virtual-Tissue Modeling Summer School and Hackathon.

Indiana University, Bloomington, Indiana.

Dates: Sunday July 26th, 2020 - Sun. Aug 9.

For more information, please see our announcement at http://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 first half covers modeling biochemical networks, including metabolic, signaling and gene regulatory networks. The second half covers multicellular modeling, which applies to developmental and tissue biology, tissue engineering, developmental diseases like cancer and tissue-level toxicology. No specific programming or mathematical experience is required.

Summer school attendance guarantees admission to the Model-Building Hackathons.

The Hackathons 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 Hackathons. 


An Introductory Python Tutorial will take place on July 26th, 2020. If you already know Python, you may skip this Tutorial or take this material as a review

Network Modeling Summer School (July 27-July 30, 2020) and Hackathon (July 31-August 2, 2020): Text on Network Modeling Here!

Multicell Virtual-Tissue Modeling Summer School (August 3-August 6, 2020) and Hackathon (August 7-August 9,2020):

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 allow researchers with modest programing 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. CompuCell3D is open source, allowing users to extend, improve, validate, modify and share the core software. By the end of the Summer Schools and Hackathons, 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.


Summer schools will include four days of lectures and hands-on computer tutorials. In the modeling Hackathons 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

Dynamic Network Modeling with Tellurium

Multicellular Virtual-Tissue simulations with CompuCell3D

Combining network models with virtual-tissue models in multiscale models


Prof. Julio Belmonte (North Carolina State University), Mr. Juliano Gianlupi (Indiana University), Prof. James A. Glazier (Indiana University), Dr. Bobby Madamanchi (Purdue University), Prof. Herbert Sauro (University of Washington, Tellurium lead developer), Dr. T.J. Sego (Indiana University, CompuCell3D lead developer), Dr. James Sluka (Indiana University), Dr. Endre Somogyi (Indiana University, Tellurium lead developer), Dr. Maciek Swat (CompuCell3D lead developer), Prof. Gilberto Thomas (Federal University of Rio Grande do Sul, Brazil)


Because the number of places is limited, admission is by application only. To apply for admission, please visit the school websitewww.compucell3d.org or email compucell3d.iu@gmail.com


April 1st, 2020. Applications will be processed as received. Please do not make travel arrangements until you have received a notice that your application for admission has been accepted.

The workshop is partially supported by grants from the US National Institutes of Health. Enrollment is free and includes breakfast and lunches. However, participants are expected to cover their own travel and accommodation costs and the optional group dinners. The workshop may be able to assist participants who are interested in sharing accommodations.


The workshop will be held in the Woodburn Hall Conference Facility, on the campus of Indiana University, Bloomington. The nearest airport to Bloomington is Indianapolis International Airport (IND). A scheduled bus service runs between IND airport and Indiana University. Numerous hotels and rental options and a wide variety of restaurants are located within walking distance of Woodburn Hall.

We look forward to welcoming you in Bloomington this July and August.

James A. Glazier

Department of Intelligent Systems Engineering

Indiana University, Bloomington


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