Abstract
The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.
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
Foster, I., Kesselman, C., Tuecke, S.: The anatomy of the grid: Enabling scalable virtual organizations. International Journal of High Performance Computing Applications 15(3), 200–222 (2001)
Ellert, M., Konstantinov, B., K’onya, J., Lindemann, J., Livenson, I., Nielsen, J., Smirnova, O., Wäanänen, A.: Advanced Resource Connector middleware for lightweight computational Grids. Future Generation Computer Systems. The International Journal of Grid Computing: Theory, Methods and Applications 23, 219–240 (2007)
Elmroth, E., Tordsson, J.: Grid Resource Brokering Algorithms Enabling Advance Reservations and Resource Selection Based on Performance Predictions. Future Generation Computer Systems. The International Journal of Grid Computing: Theory, Methods and Applications (2007)
Ellert, M., et al.: The NorduGrid project: using Globus toolkit for building GRID infrastructure. Nuclear Instruments & Methods in Physics Research Section a-Accelerators Spectrometers Detectors and Associated Equipment 502(2-3), 407–410 (2003)
Andrade, J., et al.: Using Grid technology for computationally intensive applied bioinformatics analyses. Silico Biology, 6 (2006)
Gudbjartsson, D.F., et al.: Allegro, a new computer program for multipoint linkage analysis. Nat Genet 25(1), 12–13 (2000)
Andrade, J., et al.: The use of Grid computing to drive data-intensive genetic research. European Journal of Human Genetics (March 21, 2007)
Elmroth, E., Tordsson, J.: An interoperable, standards-based Grid resource broker and job submission service. In: First International Conference on e-Science and Grid Computing, IEEE Computer Society Press, Los Alamitos (2005)
Gui, X.L., et al.: A grid security infrastructure based on behaviors and trusts. In: Grid and Cooperative Computing Gcc 2004 Workshops, Proceedings, vol. 3252, pp. 482–489 (2004)
Beckles, B., Welch, V., Basney, J.: Mechanisms for increasing the usability of grid security. International Journal of Human-Computer Studies 63(1-2), 74–101 (2005)
Blanchet, C., et al.: GPS@ Bioinformatics Portal: from Network to EGEE Grd, vol. 2006, pp. 187–193. IOS Press, Amsterdam (2006)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Andrade, J., Andersen, M., Berglund, L., Odeberg, J. (2007). Applications of Grid Computing in Genetics and Proteomics. In: Kågström, B., Elmroth, E., Dongarra, J., Waśniewski, J. (eds) Applied Parallel Computing. State of the Art in Scientific Computing. PARA 2006. Lecture Notes in Computer Science, vol 4699. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75755-9_96
Download citation
DOI: https://doi.org/10.1007/978-3-540-75755-9_96
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75754-2
Online ISBN: 978-3-540-75755-9
eBook Packages: Computer ScienceComputer Science (R0)