ACADEMIA
Pacific Rim Researchers Use Grid, Bioinformatics to Analyze Avian Flu
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- Category: ACADEMIA
- Characterize the function of the influenza viruses using a structure-based approach;
- Develop simulations of the molecular dynamics involving interactions among major factors that may determine the virulence of a virus; and
- Test whether the multinational collaboration can establish a successful, large-scale, distributed computational data grid.
Scientists at UC San Diego, the California Institute for Telecommunications and Information Technology (Calit2) and San Diego Supercomputer Center (SDSC) will use bioinformatics software, including the integrated Genome Analysis Pipeline (iGAP), to analyze avian flu genomes. (The iGAP suite of bioinformatics applications are designed specifically for protein structural homology recognition and functional annotation.) The San Diego-based researchers will also develop a robust production environment for routine computational analysis, using PRAGMA member-developed tools, including Grid Datafarm (Gfarm) and Community Scheduler Framework (CSF4), while making any new software publicly available through open-source licenses. The funding to the University of Hawaii will allow it to become a node in the computational grid – allowing it to access data for molecular-dynamics simulations using high-performance computing. “We need a better way to gain insight into the interactions among factors determining how virulent a particular type of flu might be, and this will require a lot of raw computing power,” said Maqsudul Alam, director at the Advance Studies in Genomics, Proteomics and Bioinformatics, College of Natural Sciences, University of Hawaii. “This will allow us to analyze the biosynthetic pathways of viruses as well as the signal transduction pathways for clues to understanding how avian flu interferes with human metabolism.” The Asian institutions – all members of PRAGMA – will host some U.S. students and researchers, while taking responsibility for specific tasks:
- JLU will support the scheduling of multiple clusters (CSF4) to distribute jobs transparently at multiple sites around the region;
- AIST will support the deployment of Gfarm in conjunction with researchers at the University of Tsukuba;
- KISTI in conjunction with researchers at KU in Korea will create an integrated portal environment for the computational pipeline using results of Korea National e-Science Project by the Korean Ministry of Science and Technology (MOST); and
- CNIC will develop a transparent web service layer for data access.
- USM will contribute its natural compound database for use in virtual screening for new inhibitors and drug discovery.
CNIC will also become the central repository for the project’s research data. The database will be distributed through the computational data grid, and accessible through web portals mirrored at partner sites. “The availability of a central repository that is built upon distributed information and data storage not only allows one to collect information more effectively, but also makes the data immediately available to researchers worldwide,” said Kai Nan, director of CNIC’s Network Technology and Applications Research Laboratory. “The end result is a dynamic research community response network that can meet the needs of a global response to a global threat such as the avian flu.” Much of the nitty-gritty work on the avian flu project will be done by students, at both the graduate and undergraduate level. “We’ll be engaging students from the above institutions as an international research team,” said NBCR’s Li. “We will also send U.S. students and graduate researchers to work in the labs of our partners around Asia – giving those students an experience that will equip them to do ongoing research in this field.” This activity also leverages NSF’s investment in the Pacific Rim undergraduate Education (PRIME) project, an undergraduate research abroad program awarded to UCSD. “The next step for PRAGMA is a pragmatic one – to demonstrate that international team science can address pressing challenges in a way that might not be possible in one institution or just one country,” said Arzberger. “We expect that this project will engage other researchers, both in other PRAGMA sites, e.g., at USM in Malaysia, and also at the National Biomedical Computation Resource, through the complementary, ongoing Avian flu Drug Discovery project led by professors J. Andrew McCammon and Art Olson of NBCR, by sharing expertise and resources.”