Clarkson Graduate Student Develops Tool to Help Scientists Simulate Biological Patterns
Clarkson University Electrical and Computer Engineering graduate student Olaolu Olugbenle has developed a MATLAB application that helps scientists and students simulate how spot patterns form in fruit flies — a model for understanding the formation of complex biological patterns.
The app lets users change settings such as cell size and shape to see how those changes affect the patterns that form in a virtual tissue. It’s designed to be easy to use, even for people without programming experience, so scientists and students can explore how natural patterns develop without needing to write computer code.
“I wanted to create something that bridges the gap between biology and computing,” Olugbenle said. “This app lets biologists explore how patterns emerge in living systems without needing to write code.”
Olugbenle also made the program much faster by improving how it runs on Clarkson’s High-Performance Computing (HPC) cluster. The app’s runtime for a tissue with 900 cells dropped from 1 hour and 40 minutes to just 20 minutes — a 64 percent improvement and 3.3 times faster speedup.
The MATLAB app has practical uses for both research and education. Scientists can use it to test and refine ideas before doing real experiments, saving time and materials in the lab. Students can use it to learn about how biological spot patterns form, even if they don’t have access to laboratory equipment.
“Simulation tools like this one are vital in modern biology,” said Olugbenle. “They allow researchers to test ideas virtually before committing to lengthy or costly experiments. For students, it’s an engaging way to visualize how nature organizes itself.”
The project showcases Clarkson’s commitment to interdisciplinary research and hands-on innovation, where engineering and science come together to solve complex problems. Olugbenle’s work demonstrates how computing power and creativity can make scientific exploration more efficient and accessible.
This project is part of a broader collaborative effort by Clarkson Assistant Mathematics Professor Emmanuel Asante-Asamani and Assistant Biology Professor Ginger Hunter from Howard University to understand how cells communicate over long distances to form tissue scale patterns. The project is currently supported by the National Institutes of General Medical Sciences of the National Institutes of Health.
