IEEE Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) is a bimonthly journal that publishes archival research results related to the algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology. Read the full scope of TCBB


IEEE Transactions on Computational Biology and Bioinformatics (TCBB) will move to the OnlinePlus publication model starting with 2015 issues!


From the January/February 2015 Issue

Heterogeneous Cloud Framework for Big Data Genome Sequencing

By Chao Wang, Xi Li, Peng Chen, Aili Wang, Xuehai Zhou, and Hong Yu

Featured article thumbnail imageThe next generation genome sequencing problem with short (long) reads is an emerging field in numerous scientific and big data research domains. However, data sizes and ease of access for scientific researchers are growing and most current methodologies rely on one acceleration approach and so cannot meet the requirements imposed by explosive data scales and complexities. In this paper, we propose a novel FPGA-based acceleration solution with MapReduce framework on multiple hardware accelerators. The combination of hardware acceleration and MapReduce execution flow could greatly accelerate the task of aligning short length reads to a known reference genome. To evaluate the performance and other metrics, we conducted a theoretical speedup analysis on a MapReduce programming platform, which demonstrates that our proposed architecture have efficient potential to improve the speedup for large scale genome sequencing applications. Also, as a practical study, we have built a hardware prototype on the real Xilinx FPGA chip. Significant metrics on speedup, sensitivity, mapping quality, error rate, and hardware cost are evaluated, respectively. Experimental results demonstrate that the proposed platform could efficiently accelerate the next generation sequencing problem with satisfactory accuracy and acceptable hardware cost.

download PDF View the PDF of this article      csdl View this issue in the digital library


Editorials and Announcements

Announcements

  • Get Your Journals as eBooks for Free

  • TCBB celebrates its 10th Anniversary. Editor-in-Chief Ying Xu says, "The emergence and maturation of increasingly more and powerful molecular measurement technologies such as next generation sequencing and chromosome conformation capture allow scientists to tackle biological problems at the depth and breadth that we have never seen before. At the same time the enormity and complexity of the data generated using these technologies raised tremendous challenges to computational scientists to develop more effective techniques to store, transmit, organize, process, analyze and mine the data, and to construct models to assist interpreting the data. Since its creation ten years ago, TCBB has been playing a major role in bridging the world of computing and the world of biology. I want to congratulate what the journal has done in providing biologists with the most powerful computational tools to help address their data and modeling needs. I fully expect that TCBB will continue to play increasingly significant roles in attracting more computational scientists to address the ever increasing needs for new and more powerful computational techniques and to introduce to new comers the important and challenging computational biology problems in a timely fashion."

  • Subscribe to TCBB in 2014. Click for more information. (PDF)

Editorials


Guest Editorials


Call for Papers


Reviewers List


Access All Recently Published TCBB Articles

RSS Subscribe to the RSS feed of latest TCBB content added to the digital library

Mail Sign up for the Transactions Connection newsletter.


TCBB is a joint publication of the IEEE Computer Society, Association for Computing Machinery, IEEE Computational Intelligence Society, and the IEEE Engineering in Medicine and Biology Society.

IEEE Computer Society    ACM    Computational Intelligence Society    Engineering in Medicine and Biology Society

Published in cooperation with: IEEE Control Systems Society


MEDLINE      PubMed

Indexed in MEDLINE®/PubMed® & ISI