Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation [chapter]

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
2005 Lecture Notes in Computer Science  
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
more » ... pment. 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 To whom correspondence should be addressed. Phone 858-822-1079, Fax 858-822-4767 pp. 53-67, 2005. c Springer-Verlag Berlin Heidelberg 2005 A. Konagaya and K. Satou (Eds.): LSGRID 2004, LNBI 3370, 54 A. Shahab et al. 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.
doi:10.1007/978-3-540-32251-1_6 fatcat:ik3skiae7feajo2r5k6jr7psg4