The University of Rochester Medical Center has developed a new high-tech tool that allows scientists to create models and develop simulations of complex systems, such as the interaction between the flu virus and the immune system. The developers at URMC’s Center for Biodefense Immune Modeling (CBIM) believe their “DEDiscover” software will have a broad impact on the scientific community because it enables scientists to better understand data from their current experiments and to more effectively design future experiments.
“Using models and simulations is commonplace in many industries, such as the auto and airline industries, where manufacturers test designs before they actually produce cars and planes,” said Hulin Wu, Ph.D., co-director of the center and professor in the Department of Biostatistics and Computational Biology at the Medical Center. “Biomedical research has adopted this same way of doing business, using models to gather information that will help scientists design the most effective vaccines and therapies in the shortest amount of time.” Wu added that models are essential because many experiments can’t be done in a lab: “We can’t infect people with a new strain of the flu virus, but we can use a mathematical model of a human in the computer to learn more about the virus and test potential therapies.”
“DEDiscover bridges a longtime language gap between scientists, statisticians, and mathematical modelers,” noted Associate Professor Gregory Warnes, Ph.D., who leads the CBIM software development effort. “DEDiscover’s simple controls for advanced mathematical and statistical methods allow all three groups to utilize the same software for the first time, breaking down a key communications barrier that has long impeded research progress.”
DEDiscover is already making an impact on research conducted at the Medical Center. “DEDiscover is a great software tool. I can use it to easily model immune processes, allowing me to
incorporate several new models into NIH grants,” said Martin S. Zand, M.D., Ph.D., CBIM co-director, professor of Medicine, and director of the URMC Kidney and Pancreas Transplant Program. “Good data are very hard to generate, and yet this information is critically important because it connects science to treatments. This modeling can give us profound insight into patient care, allowing us to make predictions about treatment, and most importantly, showing us why treatments may fail.”
DEDiscover is also improving the education of future researchers. “I’m using DEDiscover to teach students to apply mathematical models to biological problems, such as understanding how the body processes antidepressants,” says Stanley Dunn, Ph.D., of Rensselaer Polytechnic Institute. “It’s far easier for the students to learn DEDiscover than other software tools, and it allows them to address more complex medical issues.”
While the CBIM team developed DEDiscover to model the body’s immune response to viruses, it can be applied to many problems spanning scientific, biological, and medical disciplines. The team hopes DEDiscover will become a standard tool for helping researchers answer many difficult yet important questions, whether they arise from medicine – “Why do some patients make antibodies against a new kidney?” – from physics – “How do the concentrations of different elements in radioactive waste change over time?” – from ecology – “What is the effect of increased water temperature on the ecology of plankton?” – or from other scientific fields.
DEDiscover is available as a free download from the CBIM web site at https://cbim.urmc.rochester.edu/software/dediscover.
About the Center for Biodefense Immune Modeling
The Center for Biodefense Immune Modeling develops models and performs experiments to better understand immune responses to influenza infections and vaccinations and to develop new mathematical approaches and software tools, such as DEDiscover, for the broader research community. The CBIM was founded in 2005 with a $9.9 million contract as part of Modeling Immunity for Biodefense, a program supported by the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health. The CBIM recently received an $11.9 million contract from NIAID to continue its research through 2015.
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