August 7, 2018
NIH awards University of Washington, partner institutions $6.5M for reusable, reproducible biomedical modeling
The National Institutes of Health has awarded a $6.5 million, five-year grant to the University of Washington and partner institutions to establish the Center for Reproducible Biomedical Modeling. The center’s primary goal is to develop more effective predictive models of biological systems, which are used in research and medicine.
Herbert Sauro, a UW associate professor of bioengineering and incoming director of the Center for Reproducible Biomedical Modeling.
“We are delighted that the NIH has made this award,” said Herbert Sauro, a UW associate professor of bioengineering and incoming director of the center. “We believe the research at the center will enable credible models that can be used in the clinic to improve patient care.”
Other faculty involved with the center are John Gennari, UW associate professor of biomedical informatics and medical education; Jonathan Karr, an assistant professor of genetics and genomic sciences at the Icahn School of Medicine at Mount Sinai; Ion Moraru, professor of cell biology at the University of Connecticut; and David Nickerson, a senior research fellow in bioengineering at the University of Auckland.
The Center for Reproducible Biomedical Modeling will focus on understanding, simulating and modeling different types of biological systems, from cells and organs to whole bodies. Accurate models of these biological realms are key to advancements in precision medicine and bioengineering. At the core, these models rest on understanding how our genes interact to produce the physical characteristics of our bodies — from blood and nerve cells to lungs and toes. The number and versions of genes that we each carry — known as a genotype — play a major role in determining the physical characteristics — or phenotype — of our cells, tissues, organs and bodies. But interactions between genes and our environment, as well as the complexities of human development and disease, make predicting how genotype determines phenotype no straightforward task, which is why biologists have sought to develop accurate models of this process, said Sauro.
Announcements from partner institutions:
Models and simulations that could predict phenotype from a given genotype would help scientists understand the molecular basis of behavior, help clinicians personalize therapy and help bioengineers custom-design microbes, among other applications. But historically, researchers have lacked the tools and knowledge to develop models systematically and scalably, said Sauro.
“In addition, due to a lack of comprehensive training among researchers, few of the models used today are comprehensible, reusable and reproducible,” said Sauro. “And typically, journals do not require reported models to be reusable or reproducible.”
To enable more thorough and accurate models, the center will develop technologies to aggregate biological data systematically, scalably and collaboratively — steps that should streamline the process for designing, simulating and analyzing models. These tools developed at the center will also make biological modeling more reusable and reproducible, Sauro said. To ensure these technologies advance modeling, the center will seek input from collaborators who build models across a wide range of biological domains, scales and applications.
The center will also help organize workshops for scientists to provide assistance with annotating and verifying models submitted to partner journals. The center has already engaged recruited nine partner journals for its curation and verification services.
“We hope to establish technologies and best practices for reusable, reproducible biomedical modeling, which will advance biological modeling far beyond today’s capabilities,” said Sauro.
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For more information, contact Sauro at 206-685-2119 or hsauro@uw.edu.
Tag(s): College of Engineering • Department of Bioengineering • Herbert Sauro • School of Medicine
