A Variable-Length Network Encoding Protocol for Big Genomic Data
A Variable-Length Network Encoding Protocol for Big Genomic Data
复制标题
大基因组数据的变长网络编码协议
DOI：
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发表时间：
2016
期刊：
影响因子：
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通讯作者：
F. Saeed
中科院分区：
文献类型：
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作者：
Mohammed Aledhari;M. Hefeida;F. Saeed
现代基因组研究使用高通量仪器，可以以惊人的速度产生数据。这些使用下一代测序(NGS)机器产生的大型基因组数据集可以很容易地达到Peta级，为大规模系统生物学研究带来存储、分析和传输问题。传统网络协议对正在传输的数据视而不见，专为通用数据传输而设计。本文提出了一种新的数据感知网络传输协议来高效地传输大量基因组数据。我们的协议利用了DNA核苷酸的有限字母表，并在超文本传输协议(HTTP)框架上开发。我们的结果表明，与常规的HTTP编码方案相比，所提出的技术提高了高达84倍的传输效率。我们还证明了所得到的协议(称为VTTP)在一台机器上的性能与在10台机器上使用的BitTorrent协议相当。
Modern genomic studies utilize high-throughput instruments which can produce data at an astonishing rate. These big genomic datasets produced using next generation sequencing (NGS) machines can easily reach peta-scale level creating storage, analytic and transmission problems for large-scale system biology studies. Traditional networking protocols are oblivious to the data that is being transmitted and are designed for general purpose data transfer. In this paper we present a novel data-aware network transfer protocol to efficiently transfer big genomic data. Our protocol exploits the limited alphabet of DNA nucleotide and is developed over the hypertext transfer protocol (HTTP) framework. Our results show that proposed technique improves transmission up to 84 times when compared to normal HTTP encoding schemes. We also show that the performance of the resultant protocol (called VTTP) using a single machine is comparable to BitTorrent protocol used on 10 machines.