OSU’s investments in computing are redefining research
Tuesday, September 9, 2025
Media Contact: Sydney Trainor | Communications and Media Relations Specialist | 405-744-9782 | sydney.trainor@okstate.edu
In the last 50 years, research has shifted from lab experiments involving test tubes to computational methods using supercomputers.
This advancement in technology has revolutionized research. It allows scientists to rapidly analyze DNA sequence data, identify pathogens and conduct microbiome research more efficiently and at a higher volume.
Through critical investments in technology and expertise, Oklahoma State University’s biocomputational research spans multiple disciplines, generating insights into how living systems function at a molecular level and answering questions too difficult to answer through experiments alone.
Dr. Pratul Agarwal, associate vice president for research (Cyberinfrastructure), serves as director of OSU’s High-Performance Computing Center — a critical component of biocomputational research.
At the simplest level, Agarwal and other researchers look at genome and protein sequences and ask, “Is this a special gene?” or “What does this gene do?”
That is a biocomputational analysis called bioinformatics — information coming from biology.
“Over time, bioinformatics analysis has become very advanced. With supercomputers, it is now possible to compare entire genomes from one species to another species, one bacteria to an entire community of bacteria,” Agarwal said.
That’s on one end of the computations; on the other end, the data can be used to make models of organs and organisms. And see how they behave over time.
Currently, the pharmaceutical industry is interested in modeling air-pathways found in human lungs to determine how medications are distributed in the lungs when inhaled, according to Agarwal.
“Genes can be very unique to organisms,” Agarwal said. “By looking at certain genes, we can map out the pathogens. So, in many cases the lab-based diagnostic analysis comes from bioinformatics calculations.”
As a College of Veterinary Medicine physiological sciences professor, Agarwal studies cancer.
He is looking at an oncogene — aka mutated gene — present in humans that causes cancer when not regulated correctly. Specifically, looking at why mutations in the K-RAS protein cause a variety of cancers.
“We’re using supercomputers, computational biology, and trying to understand how we can think about designing new drugs and medication,” Agarwal said.
In 2024, Dr. Tyrell Conway, regents professor of microbiology and molecular genetics, received an NIH Institutional Development Award (IDeA) to establish a Center of Biomedical Research Excellence, creating the Oklahoma Center for Microbiome Research.
The center’s focus is on understanding microbiomes and their impact on human health.
A microbiome is a community of microorganisms, like the trillions of bacteria in our gut, each with its own DNA.
Conway’s team studies these complex mixtures by sequencing all the DNA in a sample — often from feces — and then working with Agarwal’s team to analyze the data using bioinformatics.
Each bacterial genome contains about 5 million DNA bases made up of the A, T, C and G letters you might remember from biology class, and researchers sequence each one many times over to accurately reconstruct the full genetic picture.
“Basically, we can’t do our job without the computer firepower that they bring to the job and the way that they look at computational problems,” Conway said. “It’s a resource that we can’t live without in the business of microbiome research, because the complexity of the data sets and the complexity of computing on them.”
Dr. Joy Scaria, Walter R. Sitlington Endowed Chair in Infectious Diseases in the Department of Veterinary Pathobiology, is also conducting groundbreaking microbiome research.
His team is studying the gut microbiome from various angles, including how the loss of protective microbes can lead to infections like Clostridium difficile and salmonella, how microbes or lack of might contribute to conditions like obesity, and how microbes can influence mental health and interfere with treatments for disorders like autism and depression by altering the metabolism of brain chemicals like dopamine.
Microbiology has shifted from a traditional lab science to a data-driven field, thanks to affordable sequencing, advanced computing and AI — making supercomputing infrastructure essential.
The computing power makes advanced experiments and complex hypotheses possible.
“It might sound simple asking how many species are in the gut or what a healthy microbiome looks like, but that’s actually a hard question,” Scaria said. “Think about it: we have a global population of 7 billion, and even though we’ve sampled 50,000 people, that’s still a tiny fraction.”
Analyzing gut microbiome data from tens of thousands of people produces petabyte-scale datasets that exceed the computing capacity of most labs, Scaria noted.
“Having access to the supercomputing cluster at OSU allows us to generate novel hypotheses directly from massive data analysis, which we can then rigorously test in the lab,” Scaria said.
Dr. Darren Hagen, associate professor of animal and food sciences, analyzes genomes of livestock animals to identify genetic variants causing diseases or traits.
Hagen compares genes in sheep, goats and cattle to the similarities and differences in the species.
“It dramatically sped up the results we could share with producers — what used to take a year now took just a few weeks.”
His studies involved investigating a form of dwarfism in black-faced club lambs by sequencing sheep genomes and using computing power to pinpoint a single DNA mutation out of 3.2 billion bases that caused the condition.
“It dramatically sped up the results we could share with producers — what used to take a year now took just a few weeks,” Hagen said.
Another project involves sequencing genomes from cattle, bison and their hybrids to study how DNA is spatially organized within cells. By comparing genetic folding patterns across species, tissues and parental origin, the team aims to better understand how genome structure influences gene function.
Hagen uses OSU’s supercomputer to store and process terabytes of data, crucial for his bioinformatics work.
“One of the things I love about my job is having access to so much data and storage — I don’t have to start from scratch every time, which can take months,” Hagen said. “If I think of a new question or something that interests me, chances are we already have the data to explore it. Maybe it’s not perfect, and we don’t always get the exact answer we want, but I’ve got the tools, and there’s no shortage of problems to tackle.”
None of this cutting-edge research would be possible without smart, long-term investments in technology.
To put it in perspective, the human genome alone is about three gigabytes of data — enough to fit 80 genomes on an iPhone. But researchers at OSU are analyzing data from millions of bacteria, which means working with terabytes and even petabytes of information.
OSU invested in enough data storage to hold the equivalent of 5 million hours of Netflix.
This ability to process and store genetic information more affordably and efficiently is driving a revolution in biology and health research.
“Thanks to Pratul’s office, university investment and the support from the computing team, I can focus on the research I care about instead of the behind-the-scenes stuff that keeps everything running,” Hagen said. “The real limitation isn’t the data anymore ... OSU has done a great job investing in that infrastructure, and without it, my research would be a lot slower, and I’d be spending way more time on things I don’t want to do. I just want to do the science.”
Photos By: Gary Lawson and Phil Shockley
Story By: Sydney Trainor | Research Matters Magazine