With funding from IARPA, researchers will work on next-generation computational and bioinformatics tools to screen DNA sequences.
Computational biologists in the University of Maryland Institute for Advanced Computer Studies (UMIACS) are collaborating with experts from the UMD affiliated and based Fraunhofer Center for Experimental Software Engineering and Signature Science LLC to develop new approaches and tools for screening DNA sequences that might accidently—or intentionally—be altered, resulting in a biological threat.
Mihai Pop, a professor of computer science, Todd Treangen, an assistant research scientist in UMIACS, and Adam Porter, a professor of computer science at the University of Maryland and executive director of Fraunhofer, are working closely with Signature Science, a scientific and technical consulting firm, on next-generation computational and bioinformatics tools that can quickly assess whether certain synthesized DNA strands could pose a risk.
“This is an ambitious project that will join experts in biology, bioinformatics, machine learning and software engineering,” says Pop. “The software underlying this project is extremely complex, involving an intricate chain of sophisticated software components. This chain has to work seamlessly—not only to reliably identify biological threats, but to do so under strict time and resource constraints.”
DNA synthesis has increased significantly during the past decade, Pop says, with scientists in academia and industry using automated machines to construct genes and other long strands of DNA by stringing together chemical building blocks called nucleotides in any desired sequence.
While these altered DNA strands can lead to revolutionary advances in medicine, agriculture and materials science, there is the possibility that someone could exploit synthetic DNA for harmful purposes—like creating a synthetic smallpox virus, a deadly plague that was eradicated in the late 1970s, and currently exists only in a few highly secure repositories.
UMD research is part of Signature Science’s Functional Genomic and Computational Assessment of Threats program, which is being funded by the Intelligence Advanced Research Projects Activity. The research team has identified specific tasks for each group to perform in order to create a “bioinformatics analysis pipeline,” says Treangen, an expert in developing software that can quickly and efficiently analyze large amounts of genomic data. Treangen is collaborating on the project with Dan Nasko, a postdoctoral scientist, and graduate students in the Center for Bioinformatics and Computational Biology, an interdisciplinary center in UMIACS with access to powerful computing and data storage resources.
“My group will develop software modules that can provide rapid sequence and protein structure comparisons to assess the threat potential of functional elements from short DNA sequences,” he says. “The biggest challenge will be adapting current tools—and developing new tools—to perform accurate taxonomic assignment, function prediction, and threat assignment of these sequences.”
The scientists at Fraunhofer will integrate the software modules designed by Treangen’s team into a larger software infrastructure that meets regulatory standards and can be optimized for peak performance. Fraunhofer will also create the visual dashboards needed for monitoring overall system performance.
“This is a large undertaking that requires robust proficiency in designing and integrating automated systems used for testing and validating large amounts of data very quickly,” says Porter. “Fraunhofer and UMIACS can provide that type of expertise in force.”
As the prime contractor for the $2.9M project, Signature Science will coordinate the work done by UMIACS, Fraunhofer and other team members.
This effort is supported by the U.S. Army Research Office. The content of this release does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.