Attendees used CompuCell3D to model situations like vascular tumor growth
Researchers from the Luddy School of Informatics, Computing, and Engineering hosted a week-long Multicell Virtual-Tissue Modeling Summer School and Hackathon showcasing how the flexible modeling framework of CompuCell3D can be used to include a variety of applications.
The event, which was held in a virtual format, allowed participants to learn how to develop their own models, including those focusing on the battle against COVID-19. Participants ranging from the undergraduate level to research faculty attended the online event, and they took part from the United States, China, the United Kingdom, Germany, India, Sweden, Ireland, Brazil, France, and Taiwan.
“The attendees came from backgrounds in everything from medicine to engineering to mathematics,” said James Glazier, a professor of intelligent systems engineering and one of the organizers of the event. “Everyone participates in the workshop as an equal. Collaboration is essential, because no one knows all the disciplinary material a project needs, and almost no one has prior experience in this kind of modeling. One of the undergraduates told us at the end of this year's workshop that it was her first research project, but she wound up leading a Hackathon group with more senior researchers. I hope the participants left the workshop able to conceptualize and build mechanistic computer simulations—what we call ‘Virtual Tissues’—to solve their own diverse biomedical research problems.”
Participants enjoyed workshops on Python scripting and virtual-tissue simulations, including how to model infections, immune responses, and tissue damage and recovery. The hackathon saw groups create models on topics as diverse as tissue engineering, tumor vascularization, ovary development, mosquito-carried diseases, and more.
“In general, you wouldn't expect to be able to build a model of stress fibers within a crawling cell, blood vessels in a tumor, infection of the skin by a mosquito and a growing ovary, all with the same framework,” Glazier said. “With CompuCell3D, we can see the commonality of biological processes that lets us reuse ideas and methods between seemingly unrelated projects. Almost everyone who participated in the Hackathon left with a working initial computer simulation of their problem, and extensions of these simulations can form the basis for serious research studies. I am always impressed that people who have done little or no modeling before can get to that point in just a week. I hope that the students also developed an appreciation for the diversity of problems and researchers in this field and started some unexpected research collaborations across the world.”
The workshop has been held annually for the past 15 years, but this was the first event that has been held virtually. The move was in response to the COVID-19 pandemic, but it allowed organizers to explore different formats that can be offered more frequently. For instance, T.J. Sego, a postdoctoral fellow at IU, led a pair of mini workshops focused on COVID modeling that drew more than 70 participants.
“Now that we have seen how well the virtual format can work, we’d like to definitely give another workshop sooner while also teaching some more targeted workshops focusing on advanced modelers or computer engineers who want to extend our open-source modeling framework,” Glazier said. “I really believe in the goal of helping people solve difficult scientific problems through modeling. I am always stimulated by the creative ways people find to apply CompuCell3D to problems that were new to me. I also find a lot of satisfaction in seeing new collaborations develop and seeing undergraduates—and even the occasional high-school student—participate in collaborative science on an equal footing with senior professors.”
Sessions from the CompuCell3D Multicell Virtual-Tissue Modeling Summer School workshop are available for free at the event’s website.
“These workshops and hackathon events allow the Luddy School and its faculty to play a critical role in opening the doors of understanding to a wide variety of researchers,” said Kay Connelly, associate dean for research at the Luddy School. “It’s great to see people from all over the world come together to learn this framework, and we hope they can use that knowledge to build the innovations of tomorrow.”