November 23, 2009–The University of Delaware is part of a multi-state team that has been awarded a total of more than $14 million from the National Science Foundation (NSF) and the National Institutes of Health (NIH) to improve networking capabilities among the Northeast Regional IDeA and EPSCoR states — Delaware, Maine, New Hampshire, Rhode Island and Vermont. Research leaders from these five states first came together in 2006 to launch the North East Cyberinfrastructure Consortium (NECC).

Pictured are, front, from left, Douglas O’Neal and Bruce Kingham, and back, from left, Karl Steiner and Cathy Wu.

NSF’s EPSCoR (Experimental Program to Stimulate Competitive Research) and NIH’s IDeA (Institutional Development Award) initiatives are providing strategic programs to promote the development, coordination and sharing of statewide research infrastructure and expertise that will expand the research opportunities and increase the number of competitive investigators in the EPSCoR- and IDeA-eligible states.

Awarded to the NECC states under the American Recovery and Reinvestment Act (ARRA), the two grants will provide significant funding to “light up the north,” the region north of Boston that has been referred to as a “black hole of connectivity,” and to launch new, network-intensive collaborative efforts in biomedical and environmental research and education. Delaware’s share of the total funding is about $2 million.

The Delaware effort will be led by Karl Steiner, professor in the Department of Electrical and Computer Engineering, and Cathy Wu, the Edward G. Jefferson Chair of Bioinformatics and Computational Biology and professor in the Department of Computer and Information Sciences.

According to Steiner, who is also associate provost for interdisciplinary research initiatives at UD, the goals of the project are to improve regional internet connectivity to national high-speed networks, facilitate biomedical research collaborations, provide training and education for scientists and educators, strengthen inter-institutional partnerships, and enable access to distributed research resources.

Most of the funds will be used to build a broadband fiber optics network across New England and to upgrade and improve campus-wide bandwidth and redundancy at UD and Delaware State University, so that consortium members can take full advantage of national and international cyber resources for research and education.

In addition, two new cyber-based pilot projects will be carried out through a virtual organization, the North East Bioinformatics Collaborative (NEBC), created for the sharing of expertise and facilities in the region. A successful demonstration project has been carried out through the NEBC using dogfish shark genome data collected in Maine, stored in Delaware, and annotated in Vermont to explore the efficacy of a regionally distributed datacenter model.

The two new pilot projects will enable the team to conduct meaningful research while also building the information highway and assessing its effectiveness. One of the projects will focus on determining the metagenomes of cyanobacterial blooms in lakes in the Northeast. The other will be aimed at sequencing and annotating the complete genome of the skate, a fish of increasing commercial relevance, commonly found in New England.

In the latter project, tissue preparation of the skate samples, will be conducted at Mount Desert Island Biological Laboratory (MIDBL), near Bar Harbor, Maine, and full genome sequencing will be carried out at UD under the direction of Bruce Kingham, associate scientist and director of UD’s Sequencing and Genotyping Center.

“This project will take full advantage of our recently installed Illumina high-throughput sequencer to process the samples,“ says Kingham. “The work will require significant processing, storage and bandwidth capacity, since the sequencer can generate up to a terabyte of raw data per day.”

The assembly, analysis and annotation of the genomic data will be conducted collaboratively among researchers at the Vermont Genetics Network at the University of Vermont in Burlington, at MIDBL, and at UD. The information will then be stored at two regionally distributed data centers, one at UD and the other at the University of Maine in Orono.

“This will enable us to provide valuable redundancy on data storage, while taking advantage of complementary scientific expertise at our partner institutions in the Northeast,” says Douglas O’Neal, manager of the Bioinformatics Center at the Delaware Biotechnology Institute (DBI), which serves as one of the two data centers.

Steiner emphasizes that the pilot projects are just examples of a myriad of cyber-enabled research projects that can be carried out once the resources are fully developed. “The beauty of a well-developed cyberinfrastructure,” he says, “is that its impact is not limited to human health, the environment, or energy. It provides a basic but critical platform on which research in any field can be developed.”

Wu — who is a national expert in bioinformatics, an emerging field where information and biology converge — says that shared data systems and computational resources are critical to cutting-edge research in genomics and the key to regional collaborations. Wu’s leadership of the Protein Information Resource — an integrated protein informatics resource for genomic, proteomic, and systems biology research — will be an important asset to the new project.

Along with Prof. Carolyn Mattingly at MIDBL, Wu will lead a training program for bioinformatics workforce development that will interface directly with the skate genome-sequencing project. Focusing on distributed genome annotation, the program will allow students and junior investigators to learn major bioinformatics concepts, approaches, and resources and to participate in community genome annotation alongside senior scientists and database curators.

“This type of cyber-based sequencing and annotation reflects the way we need to conduct our research in the future,” Wu says. “Collaborations with our colleagues in Vermont, Maine, and the other NECC states will add tremendous value as we pursue our scientific goals.”

The collaboration will also encompass a multi-state educational component for high school and undergraduate students. Drawn from the five NECC states as well as New York and Puerto Rico, the students will work on a comprehensive watershed-monitoring project. The entire group will meet through multi-media videoconferencing to learn about watershed sampling, sample analysis, database creation, modeling, and environmental monitoring and analysis and to participate in career opportunity panels.

In addition, Delaware will utilize the enhanced cyberinfrastructure to develop the first stage of a centralized Delaware Environmental Monitoring and Analysis Center that will utilize the enhanced cyberinfrastructure to improve remote access to environmental sensors and monitoring stations across the state to analyze and assess environmental conditions in real time.

“We are particularly delighted that both NSF and NIH have worked closely with us as we outline the cyberinfrastructure needs across our states and developed the NECC vision,” Steiner says. “These two federal agencies have accepted the challenge and have become great partners by helping us build both the broadband ‘cyber-road’ and the connections among people needed to put ‘research traffic’ on it.”

“None of the states in the NECC consortium has all of the resources required to conduct this kind of work by themselves,” he adds, “but if we pool our resources, we can accomplish these projects and compete on the national level.”

The new funding will complement support provided through NSF’s EPSCoR RII (Research Infrastructure Improvement) program and NIH’s COBRE (Centers of Biomedical Research Excellence) and INBRE (IDeA Network of Biomedical Research Excellence) programs via NIH’s National Center for Research Resources (NCRR).

“Our states are successfully building biomedical research infrastructure through INBRE and COBRE,” says David Weir, director of UD’s Office of Economic Innovation and Partnerships and principal investigator of the Delaware INBRE program, “but the ultimate success of this work hinges on having good regional cyber-connectivity to foster collaboration and sharing of resources. The enhanced fiber network will dramatically increase our capacity for important collaborative initiatives in biomedical research, education and workforce development.”

Article by Diane Kukich in UDaily
Photo by Ambre Alexander