Abstract
Linkage analysis is a tool used by geneticists for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However analyses of large inbred pedigrees with extensive missing data are often beyond the capabilities of a single computer. We present a distributed system called superlink-online for computing multipoint LOD scores of large inbred pedigrees. It achieves high performance via efficient parallelization of the algorithms in superlink, a state-of-the-art serial program for these tasks, and through utilization of thousands of resources residing in multiple opportunistic grid environments. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either installation of software, or maintenance of a complicated distributed environment. The main algorithmic challenges have been to efficiently split large tasks for distributed execution in a highly dynamic non-dedicated running environment, as well as to utilize resources in all the available grid environments. Meeting these challenges has provided nearly interactive response time for shorter tasks while simultaneously serving massively parallel ones. The system, which is being used extensively by medical centers worldwide, achieves speedups of up to three orders of magnitude and allows analyses that were previously infeasible.
This work is supported by the Israeli Ministry of Science.
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Silberstein, M., Geiger, D., Schuster, A. (2007). A Distributed System for Genetic Linkage Analysis. In: Dubitzky, W., Schuster, A., Sloot, P.M.A., Schroeder, M., Romberg, M. (eds) Distributed, High-Performance and Grid Computing in Computational Biology. GCCB 2007. Lecture Notes in Computer Science(), vol 4360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69968-2_9
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