Grid portal interface for interactive use and monitoring of high-throughput proteome annotation

  • Authors:

  • Atif Shahab;Danny Chuon;Toyotaro Suzumua;Wilfred W. Li;Robert W. Byrnes;Kouji Tanaka;Larry Ang;Satoshi Matsuoka;Philip E. Bourne;Mark A. Miller;Peter W. Arzberger

  • Affiliations:

  • Bioinformatics Institute, Singapore;Bioinformatics Institute, Singapore;Dept. of Mathematical and Computing Sciences;Research and Development for Applied Advanced Computational Science and Technology, Japan Science and Technology Agency, Saitama, Japan;Research and Development for Applied Advanced Computational Science and Technology, Japan Science and Technology Agency, Saitama, Japan;Global Scientific Information and Computing Center;Bioinformatics Institute, Singapore;Dept. of Mathematical and Computing Sciences;Research and Development for Applied Advanced Computational Science and Technology, Japan Science and Technology Agency, Saitama, Japan;Research and Development for Applied Advanced Computational Science and Technology, Japan Science and Technology Agency, Saitama, Japan;Life Sciences Initiatives, University of California, San Diego, La Jolla, CA

  • Venue:
  • LSGRID'04 Proceedings of the First international conference on Life Science Grid
  • Year:
  • 2004

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Abstract

High-throughput proteome annotation refers to the activity of extracting information from all proteins in a particular organism using bioinformatics software on a high performance computing platform such as the grid. The Encyclopedia of Life (EOL) project [1] aims to catalog all proteins in all species for public benefits using an Integrative Genome Annotation Pipeline [2] (iGAP). The intrinsic complexity of the pipeline makes iGAP an ideal life sciences application to drive grid software development. It is a flagship application for the TeraGrid project [3]. The deployment of iGAP on the grid using grid middleware and mediator software has been described previously [4]. The heterogeneous and distributed computing environment on the grid requires an interactive user interface where jobs may be submitted and monitored. Here we describe our international collaborative effort in creating a grid portal solution for grid computing in life sciences under the auspices of PRAGMA [5]. Specifically, the development of GridMonitor for interactive monitor of iGAP workflow, and the use of a GridSpeed [6] generated iGAP application portal are described. The portal solution was part of the EOL demonstration at Supercomputing 2003 (SC'03) [7], where resources from 6 institutions on 5 continents are utilized to annotate more than 36,000 proteins from various species. It is a testimony to the necessity and expediency for international collaboration in an increasingly global grid computational environment to advance life sciences research.