The U.S. Centers for Disease Control and Prevention has funded research by a team of Penn State scientists to strengthen infectious disease surveillance, detection, and preparedness by developing an accessible bioinformatics platform and tools for utilization by the CDC’s Laboratory Response Network.
The Laboratory Response Network is a linked system of labs across the country that rapidly responds to biological and chemical threats and public health emergencies. The Penn State team will provide the network with an accessible software platform and tools for whole-genome sequencing data analyses and interpretation of results, according to team principal investigator Jasna Kovac, assistant professor of food science.
Genomics approaches can be leveraged for the detection of known and novel infectious agents, including emerging infectious disease pathogens explained Kovac, who is also the Lester Earl and Veronica Casida Career Development Professor of Food Safety in the College of Agricultural Sciences.
“In this project, our team is partnering with the CDC to assess machine-learning-based approaches for the detection of potential novel pathogens,” she said. “We will evaluate the performance of multiple machine learning-based pathogen-prediction models. The performance of these models will be assessed on a set of Bacilli genomes that we whole-genome sequenced over the past year.”
Under the leadership of team co-principal investigator Greg Von Kuster, Penn State Galaxy Consultant, working out of the University’s Huck Institutes for the Life Sciences, the team will develop a Galaxy environment to enable CDC Laboratory Response Network scientists to conduct near real-time bioinformatic analyses and produce actionable information.
Von Kuster, who has been working in computational research for 34 years and is one of the initial developers of the Galaxy project, is an expert in data-intensive computational research using Galaxy. Galaxy is an open-source, web-based platform for data-intensive biomedical research, enabling non-bioinformaticians to conduct complex bioinformatics analyses.
“Penn State scientists began developing Galaxy in 2005, and the Galaxy team has expanded to a worldwide community with continuous ongoing enhancements,” he said. “Galaxy has been adopted and utilized around the world by thousands of scientists, across many areas of research. It will significantly enhance the research being conducted by the CDC’s Laboratory Response Network.”
The Galaxy platform will enable integration of the established CDC bioinformatics workflows with the pathogen-prediction workflows that will be developed in this project.
Also on the Penn State research team are Taejung Chung and Xiaoyuan Wei, doctoral degree student and a postdoctoral scholar respectively in the Department of Food Science; and Nate Coraor, system administrator, programmer on the Galaxy Team, Department of Biochemistry and Molecular Biology.
