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SICE hosts CompuCell3D User Training Workshop

2018-08-22
CompuCell3D Training

The School of Informatics, Computing, and Engineering hosted the 13th CompuCell3D and SBW User Training Workshop Aug. 5-11, which welcomed a diverse group of 22 students from around the nation and the world to learn to develop multi-scale Virtual Tissue Simulations using CompuCell3D software.

The CompuCell3D modeling software is an open-source environment that 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. The workshop featured lectures and hands-on tutorials, and it provided an opportunity for attendees to present a lightning talk on his or her problem of interest.

"We teach people how to model the ways cells organize themselves to form tissues and organisms," said James Glazier, a professor of intelligent systems engineering at SICE and the director of the Biocomplexity Institute at IU. "There are multiple classes of projects the attendees work on, from modeling how tissues and organisms grow to how they maintain themselves to how they react to disease. We've used the software for all of these purposes, and we try to teach them to create a basic simulation that will allow them to model their specific problem."

Attendees came from a range of backgrounds, including chemical engineering, mechanical engineering, pathology, applied mathematics, electrical engineering, mathematics, physics, and biomedical engineering. The group included people with experience ranging from the high school level through undergraduate, graduate, post-doc, and full professors.

Participants came to Bloomington from as close as IU Bloomington, Purdue, IUPUI, and Notre Dame to as far away as the University of Texas, the University of Southern California, MIT, Morehouse College, and King's College in London, among other places.

"It's about as diverse a bunch as you can get," Glazier said. "They came from all over. It was a good group and really shows the accessibility of the workshop. We want to be training a highly diverse group of future engineers, and we're proud of the diversity that we hosted on campus."

In addition to developing tissue models, the workshop also covered the Systems Biology Workbench (SBW) used to create Reaction-Kinetic models. Attendees will receive post-workshop support and opportunities for collaboration to continue using these simulation environments in their research projects.

For more information on intelligent systems engineering at SICE, visit our website.

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