UF Health to house mathematical BioModels database

GAINESVILLE, Fla. — BioModels, an open-access database used by scientific researchers to share their mathematical models with other scientists, is crossing the pond for a new home at the University of Florida.

BioModels, launched in the United Kingdom in 2005, is a massive repository that allows researchers to exchange, reuse and repurpose mathematical models. In short, it keeps biological scientists from having to start from scratch anytime they begin a new study.

It now houses nearly 2,750 models and grows by the day.

BioModels is in essence a “digital ecosystem” for scientists, said T.J. Sego, Ph.D., an assistant professor in pulmonary systems medicine in the College of Medicine. The database is FAIR, Sego said, “findable, accessible, interoperable and reusable.”

It is such a foundational resource, Sego said, that “when we have a system that we’re interested in and are considering developing a model for, the first thing we’ll do is go to BioModels and see if one already exists.”

By late 2025, BioModels will be housed in the Laboratory for Systems Medicine, a “natural home” thanks to the intense amount of computational work the lab does, Sego said.

Reinhard Laubenbacher, Ph.D., the laboratory’s director and a mathematician, said model-based design using computational models is common in engineering.

“The reason it’s possible to design an entire jetliner on the computer is precisely because you have a lot of standardized models for all of the different components that you can connect together and build bigger pieces from,” he said. “And that has been a revolution in engineering design. In medicine, the big picture would be for us to get to the same place.”

As a tangible example, Laubenbacher’s lab has worked for years to build a digital replica of the body’s immune response to respiratory infections caused by microbes, bacteria and viruses. Someday, they expect to use a patient’s medical data in that digital twin to create a personalized treatment plan.

A digital twin would be precisely the sort of computational model that could be housed in BioModels, Laubenbacher said.

“So that’s what I think in 10 years, or 15 years, will become a reality,” he said. “To me, the really appealing thing is that BioModels is a community resource. It’s not a commercial enterprise; there’s no money to be made.”

Hiring scientists who can build models, however, is expensive. And that’s where grants can fill the gaps, Laubenbacher said.

To understand why the prestigious database is moving to UF Health, one need look no further than a faculty member with ties both to Gainesville and Cambridge: Rahuman Sheriff, Ph.D. He is an affiliate associate professor in pulmonary medicine at UF’s College of Medicine and a senior project leader at the European Bioinformatics Institute, part of the European Molecular Biology Laboratory.