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Pacific Rim researchers to collaborate on distributed bioinformatics analysis of avian flu

PRAGMA 12 workshop.

Flu vaccines are usually developed using attenuated viruses, but the new focus is on the use of reverse genetics techniques to combat emerging bird flu pandemic threats. To that end, researchers intend to:

  • 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 pathway
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Source:University of California - San Diego


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