文章基本信息

标题：Parallel biocomputing
本地全文：下载
作者：Kenneth S Kompass ; Thomas J Hoffmann ; John S Witte 等
期刊名称：Source Code for Biology and Medicine
印刷版ISSN：1751-0473
电子版ISSN：1751-0473
出版年度：2011
卷号：6
期号：1
页码：4
DOI：10.1186/1751-0473-6-4
语种：English
出版社：BioMed Central
摘要：With the advent of high throughput genomics and high-resolution imaging techniques, there is a growing necessity in biology and medicine for parallel computing, and with the low cost of computing, it is now cost-effective for even small labs or individuals to build their own personal computation cluster. Here we briefly describe how to use commodity hardware to build a low-cost, high-performance compute cluster, and provide an in-depth example and sample code for parallel execution of R jobs using MOSIX, a mature extension of the Linux kernel for parallel computing. A similar process can be used with other cluster platform software. As a statistical genetics example, we use our cluster to run a simulated eQTL experiment. Because eQTL is computationally intensive, and is conceptually easy to parallelize, like many statistics/genetics applications, parallel execution with MOSIX gives a linear speedup in analysis time with little additional effort. We have used MOSIX to run a wide variety of software programs in parallel with good results. The limitations and benefits of using MOSIX are discussed and compared to other platforms.
关键词：Parallel Computing ; Vanilla ; Parallel Execution ; Expression Trait ; Commodity Hardware