Document Type
Article
Publication Date
2018
College/Unit
Eberly College of Arts and Sciences
Department/Program/Center
Not Listed
Abstract
Background: The clinical decision support system can effectively break the limitations of doctors’ knowledge and reduce the possibility of misdiagnosis to enhance health care. The traditional genetic data storage and analysis methods based on stand-alone environment are hard to meet the computational requirements with the rapid genetic data growth for the limited scalability.
Methods: In this paper, we propose a distributed gene clinical decision support system, which is named GCDSS. And a prototype is implemented based on cloud computing technology. At the same time, we present CloudBWA which is a novel distributed read mapping algorithm leveraging batch processing strategy to map reads on Apache Spark.
Results: Experiments show that the distributed gene clinical decision support system GCDSS and the distributed read mapping algorithm CloudBWA have outstanding performance and excellent scalability. Compared with state-of-the-art distributed algorithms, CloudBWA achieves up to 2.63 times speedup over SparkBWA. Compared with stand-alone algorithms, CloudBWA with 16 cores achieves up to 11.59 times speedup over BWA-MEM with 1 core.
Conclusions: GCDSS is a distributed gene clinical decision support system based on cloud computing techniques. In particular, we incorporated a distributed genetic data analysis pipeline framework in the proposed GCDSS system. To boost the data processing of GCDSS, we propose CloudBWA, which is a novel distributed read mapping algorithm to leverage batch processing technique in mapping stage using Apache Spark platform.
Keywords: Clinical decision support system, Cloud computing, Spark, Alluxio, Genetic data analysis, Read mapping
Digital Commons Citation
Xu, Bo; Li, Changlong; Zhuang, Hang; Wang, Jiali; Wang, Qingfeng; Wang, Chao; and Zhou, Xuehai, "Distributed gene clinical decision support system based on cloud computing" (2018). Faculty & Staff Scholarship. 1274.
https://researchrepository.wvu.edu/faculty_publications/1274
Source Citation
Xu, B., Li, C., Zhuang, H., Wang, J., Wang, Q., Wang, C., & Zhou, X. (2018). Distributed gene clinical decision support system based on cloud computing. BMC Medical Genomics, 11(S5). https://doi.org/10.1186/s12920-018-0415-1
Comments
© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.