Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers
Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers
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DOI：
10.1086/504158
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发表时间：
2006-06-01
影响因子：
9.8
通讯作者：
Geiger, D.
中科院分区：
文献类型：
--
作者：
Silberstein, M.;Tzemach, A.;Geiger, D.
LOD得分的计算是一个有价值的工具，在孟德尔和复杂疾病的研究疾病易感基因定位。然而，计算精确的多点可能性的大型近交系广泛的缺失数据往往是超出了一台计算机的能力。我们提出了一个分布式系统，称为“超级链接在线”，用于计算多点LOD分数的大型近交系。它实现了高性能，通过有效的并行化的算法在超级链接，一个国家的最先进的串行程序，这些任务，并通过使用的空闲周期的数千台个人计算机。算法的主要挑战是如何在高度动态、非专用的运行环境中高效地拆分大型任务以进行分布式执行。值得注意的是，该系统可以在线使用，从而可以进行计算密集型分析，而无需安装软件或维护复杂的分布式环境。随着该系统的开发，它被广泛的测试，由世界各地的合作医疗中心对各种真实的数据集，其中一些是在这篇文章中。
Computation of LOD scores is a valuable tool for mapping disease-susceptibility genes in the study of Mendelian and complex diseases. However, computation of exact multipoint likelihoods of large inbred pedigrees with extensive missing data is often beyond the capabilities of a single computer. We present a distributed system called "SUPERLINK-ONLINE," for the computation of multipoint LOD scores of large inbred pedigrees. It achieves high performance via the efficient parallelization of the algorithms in SUPERLINK, a state-of-the-art serial program for these tasks, and through the use of the idle cycles of thousands of personal computers. The main algorithmic challenge has been to efficiently split a large task for distributed execution in a highly dynamic, nondedicated running environment. Notably, the system is available online, which allows computationally intensive analyses to be performed with no need for either the installation of software or the maintenance of a complicated distributed environment. As the system was being developed, it was extensively tested by collaborating medical centers worldwide on a variety of real data sets, some of which are presented in this article.