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The application of the Hadoop softwa...

Wang, Dan.

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The application of the Hadoop software framework in Bioinformatics programs.

Record Type:	Electronic resources : Monograph/item
Title/Author:	The application of the Hadoop software framework in Bioinformatics programs./
Author:	Wang, Dan.
Published:	Ann Arbor : ProQuest Dissertations & Theses, : 2016,
Description:	110 p.
Notes:	Source: Dissertation Abstracts International, Volume: 78-02(E), Section: B.
Contained By:	Dissertation Abstracts International78-02B(E).
Subject:	Information technology. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=10149201
ISBN:	9781369043198

The application of the Hadoop software framework in Bioinformatics programs.
Wang, Dan.

The application of the Hadoop software framework in Bioinformatics programs. - Ann Arbor : ProQuest Dissertations & Theses, 2016 - 110 p.

Source: Dissertation Abstracts International, Volume: 78-02(E), Section: B.

Thesis (Ph.D.)--Purdue University, 2016.

The project described in this dissertation proposal attempted to improve the efficiency and scalability performance as well as the usability and user experience of three Bioinformatics applications - DNA/peptide sequence similarity comparison, digital DNA library subtraction, and DNA/peptide sequence de-duplication - by 1) adopting the Hadoop MapReduce algorithms and distributed file system and 2) implementing the fully automated Hadoop programs into a user friendly graphical user interface (GUI). In addition, the researcher was also interested in investigating the advantages and limitations of applying the Hadoop software framework as a general methodology in parallelizing Bioinformatics programs.

ISBN: 9781369043198Subjects--Topical Terms:

532993
Information technology.

The application of the Hadoop software framework in Bioinformatics programs.
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500 $a Source: Dissertation Abstracts International, Volume: 78-02(E), Section: B.
500 $a Adviser: John Springer.
502 $a Thesis (Ph.D.)--Purdue University, 2016.
520 $a The project described in this dissertation proposal attempted to improve the efficiency and scalability performance as well as the usability and user experience of three Bioinformatics applications - DNA/peptide sequence similarity comparison, digital DNA library subtraction, and DNA/peptide sequence de-duplication - by 1) adopting the Hadoop MapReduce algorithms and distributed file system and 2) implementing the fully automated Hadoop programs into a user friendly graphical user interface (GUI). In addition, the researcher was also interested in investigating the advantages and limitations of applying the Hadoop software framework as a general methodology in parallelizing Bioinformatics programs.
520 $a After considering the original calculation algorithms in the serial version of the programs, the available computational resources, the nature of the MapReduce framework, and the optimization of performance, a processing pipeline with one pre-processing step, three mappers, two reducers and one post-processing step was developed. Then a GUI interface that enabled users to specify input/output files and program parameters was created. Also implanted into the GUI were user friendly features such as organized instruction, detailed log files, multi-user accessibility, and so on.
520 $a The new and fully automated Hadoop Bioinformatics toolkit showed execution efficiency comparable with their MPI counterparts with median to large scale data, and better efficiency than MPI when ultra-large dataset was provided. In addition, good scalability was observed with testing dataset up to 20 Gb.
590 $a School code: 0183.
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