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Drs. Paul Medvedev and Anton Nekrutenko Selected as Recipients of College of Engineering Multidisciplinary Research Seed Grant

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The College of Engineering recently awarded funding to four projects submitted to theMultidisciplinary Research Seed Grant Program.  Established in 2014, the program aims to help faculty attract high-impact multidisciplinary and center-level research funding from the state and federal government.  The program received 37 proposals this year and selected four for funding.

Paul Medvedev, faculty in Biochemistry and Molecular Biology and Computer Science and Engineering, and Anton Nekrutenko, faculty in Biochemistry and Molecular Biology, were selected to receive funding for their proposal to develop a framework that would allow scientists to query existing databases of already collectedexperimental data.  There are many scientists conducting experiments and generatingDr. Nekrutenko lots ofdata for the specific species they are researching.  This data is then usually deposited in to a public database.  These databases then become troves of useful data, but the fact is that they are not easily searchable and therefore data can go missed and unfound.  Often when conducting an experiment a researcher will ask specific questions regarding their gene of interest, but in generating the data related to their gene of interest they also generate lots of data related to other genes as well.  Often times, because the researcher is only interested in the data related to the gene they are researching, the other data simply remains in the public database until another researcher goes looking for it.

The reality is that there is tons of data located in these public databases that could be very useful to other researchers who are conducting experiments and researching other genes.  This information could be used so that researchers would not necessarily have to conduct experiments in order to obtain information that has already been obtained.  The problem is that these databases are very difficult to navigate and information can be very hard to find.  If a researcher wanted to know which of the thousands of experiments located in these public databases contained information about “Gene X” there is currently no efficient way to query that information.

Dr. Medvedev and Dr. Nekrutenko’s proposal to develop a framework in which to search the many databases that exist would allow for queries of thousands of experiments in minutes, where it currently would take years in which to collect this data.  The proposal aims to develop a search engine, similar to that of Google, for a huge internet of scientific data in science databases that cannot currently be searched.

Dr. Anton Nekrutenko currently runs and is one of the developers of the Galaxy Platform.  The Galaxy Platform is a web server for biologists to run computational methods of date.  The platform is already in place and is accessible to anyone with a web browser.  The framework Medvedev and Nekrutenko are developing would integrate into the existing platform.

Drs. Medvedev and Nekrutenko plan to submit additional grants requesting funding to the National Science Foundation (NSF) and the National Institutes of Health (NIH) for their project, as it cannot all be completed within one year.  In order to do this they will have to obtain preliminary results and develop a working prototype.  The funds received through the Multidisciplinary Research Seed Grant Program will be used to obtain these results and develop their prototype.  The prototype will be built initially on a smaller scale and then will be scaled up.  This prototype will serve as a method by which more funding can be obtained in an effort to develop their fully functional framework.