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16th Annual Multicell Virtual-Tissue Modeling On-Line Summer School and Hackathon

  • 1 Aug 2021
  • 8 Aug 2021
We are pleased to announce the 16th Annual Multicell Virtual-Tissue Modeling On-Line Summer School and Hackathon -- 2021, which will take place between Sunday August 1st, 2021 and Sun. August 8th, 2021. This workshop should be of interest to many ESMTB members. We would very much appreciate your help letting your colleagues and students know about this opportunity. A poster announcing the workshop is attached.

For more information, please see our announcement at https://compucell3d.org/Workshop21

To register, please visit: www.tinyurl.com/557ve5se 


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 August 1st, 2021. 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 2nd - August 6th, 2021) and Hackathon (August 7th  -August 8th, 2021):

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 on-line 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.


SCHOOL OVERVIEW:

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.


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. Julio Belmonte (North Carolina State University), Mr. Juliano Gianlupi (Indiana University), Prof. James A. Glazier (Indiana University), Prof. Bobby Madamanchi (University of Michigan), 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)


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 or email compucell3d.iu@gmail.com


DEADLINE for APPLICATIONS:

June 1st, 2021. 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 on line this August.

James A. Glazier

Department of Intelligent Systems Engineering

Indiana University, Bloomington

jaglazier@gmail.com




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