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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
The Encyclopedia of Life Project, http://eol.sdsc.edu
Li, W.W., Quinn, G.B., Alexandrov, N.N., Bourne, P.E., Shindyalov, I.N.: A comparative proteomics resource: proteins of Arabidopsis thaliana. Genome Biol 4, R51 (2003)
TeraGrid, http://www.teragrid.org
Li, W.W., et al.: The Encyclopedia of Life Project: Grid Software and Deployment. New Generation Computing (2004) (in Press)
Birnbaum, A., et al.: Grid Workflow Software for High-Throughput Proteome Annotation Pipeline. In: Life Sciences Grid Workshop Proceedings (2004) (Submitted)
GridSpeed, http://www.gridspeed.org
Supercomputing (2003), http://www.sc-conference.org/sc2003/
Casanova, H., Berman, F.: Grid Computing: Making the Global Infrastructure a Reality. Wiley Publishers, Inc., West Sussex (2003) (Berman, F., Fox, G.C., Hey, A.J.G. (eds.))
Pacific Rim Applications and Grid Middleware Assembly, http://www.pragma-grid.net/
Cactus Project — An open source problem solving environment, http://www.cactuscode.org/Presentations/GridPortals_2000.ppt
Grid Compute Environment (GCE) Research Group-Global Grid Forum, http://www.computingportals.org
The Astrophysics Simulation Collaboratory (ASC), https://www.ascportal.org
NPACI HotPage Grid Computing Portal, http://hotpage.paci.org
Thomas, M., et al.: The GridPort Toolkit Architecture for Building Grid Portals. In: The 10th IEEE Intl. Symp. on High Perf. Dist. Comp.
Novotny, J.: Concurrency and Computation: Practice and Experience, 1129–1144 (2002)
Commodity Grid Kits, http://www-unix.globus.org/cog/
The Globus Alliance, http://www.globus.org
Perl CoG, https://gridport.npaci.edu/cog/
von Laszewski, G., Foster, I., Gawor, J., Lane, P.: A Java Commodity Grid Kit. Concurrency and Computation: Practice and Experience 13, 643–662 (2001)
GridSphere, http://www.gridsphere.org
GridLab, http://www.gridlab.org
OGCE: Open Grid Computing Environment, http://www.ogce.org/index.php
The MyGrid Project, http://www.ebi.ac.uk/mygrid/
Suzumura, T., Nakada, H., Matsuoka, S.: GridSpeed: A Web-based Grid Portal Generation Server. In: CCGrid (Poster)
Litzkow, M., Livny, M., Mutka, M.: Condor - a hunter of idle workstations. In: Proceedings of the 8th International Conference of Distributed Computing Systems, pp. 104–111 (June 1988)
Allcock, W., et al.: GridFTP: Protocol Extension to FTP for the Grid, Grid Forum Internet-Draft (March 2001)
The Storage Resource Broker, http://www.npaci.edu/dice/srb
UNiform Interface to COmputing REsources (UNICORE), http://www.unicore.de/
JBOSS, http://www.jboss.org
NSF Middleware Initiative, http://www.nsf-middleware.org/
NPACIgrid, http://npacigrid.npaci.edu/
Workflow Management Research Group, http://www.isi.edu/~deelman/wfm-rg/
The Apache Jakarta Project, http://jakarta.apache.org
OGSA-Data Access and Integration, http://www.ogsadai.org.uk/
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Shahab, A. et al. (2005). Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation. In: Konagaya, A., Satou, K. (eds) Grid Computing in Life Science. LSGRID 2004. Lecture Notes in Computer Science(), vol 3370. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-32251-1_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-32251-1_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25208-5
Online ISBN: 978-3-540-32251-1
eBook Packages: Computer ScienceComputer Science (R0)