USD professor receives NSF grant for gene project

USD professor receives NSF grant for gene project Carol Lushbough of The University of South Dakota has received a $370,000 grant from the National Science Foundation to develop a way for scientists to easily search and analyze genetic sequence information stored in research databases across the country.

The two-year grant is part of a larger NSF grant of over a million dollars that The University of South Dakota shares in collaboration with Iowa State University.

Lushbough says that as scientists complete the genetic sequencing of various plants and animals, it becomes important for researchers to be able to compare genetic information between different species. For example, scientists often need to determine whether a particular gene they are studying in one species also appears in other species. There is currently no easy way to compare information stored in genetic databases of various plants and animals because they are not integrated.

"We're trying to create a generalized solution," said Lushbough, an assistant professor in the Department of Computer Science. "With our system, a researcher will be able to search and analyze data stored in multiple genetic databases through a single user interface. It is challenging because research institutions use a wide range of database protocols that this project must mesh together seamlessly."

Lushbough adds that, although the idea of a "federated" database in not new, this project's approach is unique. The only other institution working on a similar system and computer architecture is MIT.

In the first year, the system will link researchers to information on three selected plant databases developed at Iowa State, including rice and maize. Lushbough says the system should also be adaptable to other plant and animal species, and to any science discipline that uses multiple unconnected databases that cannot currently be accessed in a single search.

Having earned master's degrees in computer science and mathematics at USD and worked as a software engineer for VisualMetrics Corp. and Gateway Inc., Lushbough is uniquely qualified for this project.

"As the software designer for the project, my background in the field was the reason I am able to participate in the grant," Lushbough said.

Part of the grant funds two graduate assistants who work with Lushbough on the project.

"It's a growing field with a lot of opportunity," she said, "and it's great for the Department of Computer Science to be able to participate in this project."

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