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DynamicBLAST

Basic Local Alignment Search Tool (BLAST) is a heavily used bioinformatics application that has gotten significant attention from the high performance computing community. In the context of the DynamicBLAST project, BLAST execution was taken a step further by enabling it to execute on grid resources. Adapting BLAST to execute on the grid brings up concerns regarding grid resource heterogeneity, which inevitably cause difficulty with application availability, fault tolerance, interoperability, and variability in performance of individual segments that are being distributed throughout grid resources. In addition, difficulties arise because of tools, technologies, and middleware dependencies that an application developer must deal with. Dynamic BLAST is a BLAST-specific metascheduler; a multithreaded, master-worker type application that handles all aspects of a BLAST job submission on the grid for the user. It was developed with the goal of bringing the grid closer to a typical scientist by eliminating the initial learning curve necessary for use of many grid applications. Furthermore, it focuses on not only coping with grid resource heterogeneity bur rather leveraging it to improve application performance.

Features

  • Simple job submission, requiring only BLAST input query file and selection of desired parameters
  • Implemented on top of Globus Toolkit and GridWay, thus evolving automatically with the advances of those projects
  • Implementation using OGF DRMAA standard to guarantee portability and maintainability over time
  • Multi-threaded for performance and scalability
  • Built alongside Application Information Services (AIS), namely AppDB and GridAtlas, to enable explotiation of resource-application relationships
  • Improves performance of BLAST jobs up to 50% in terms of job turnaround time through 40% increase in resource utilization
  • Implements a BLAST-specific analytical performance model that allows it to cope with multitude of heterogeneous resource components

People

Publications and Presentations

  • Afgan E., Bangalore P., “Experiences with developing and deploying Dynamic BLAST”, Mardi Gras Conference 2008 – Workshop on Grid-Enabling Applications, New Orleans, LA, January 31-February 2, 2008. PDF
  • Afgan E., Sathyanarayana P., Bangalore P., “Dynamic Task Distribution in the Grid for BLAST”, IEEE GrC 2006, Atlanta, GA, May 10-12, 2006. PDF
  • Title: “UABgrid Dynamic BLAST: Searching Nucleotide and Protein Databases Using SURAgrid”, Internet 2 Meeting – Fall 2006, Chicago, IL, December 3-7, 2006. Presentation in PDF
  • Title: “Dynamic BLAST – An Approach to Dynamic Grid Application Development”, GlobusWORLD 2006, Washington, D.C., September 11-15, 2006. Presentation in PDF
  • Title: “Dynamic Task Distribution in the Grid for BLAST”, UAB Graduate Student Research Days, Birmingham, AL, March 4, 2006. Presentation in PDF

Additional links and documents

  • Sample execution of Dynamic BLAST v0.6 -> video (when video pauses, click on the ‘Play’ button to continue)