A Distributed-Processing System for Accelerating Biological Research Using Data-Staging

• Item type: Trans(1)
• 公開日: 2008-03-15
• タイトル: A Distributed-Processing System for Accelerating Biological Research Using Data-Staging
• タイトル / 言語: en
• タイトル: A Distributed-Processing System for Accelerating Biological Research Using Data-Staging
• 言語: eng
• キーワード / 主題Scheme: Other
• キーワード / 主題: Original Papers
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_6501
• 資源タイプ: journal article
• 著者所属: Graduate School of Information Science and Technology Osaka University
• 著者所属: Graduate School of Information Science and Technology Osaka University
• 著者所属: Graduate School of Information Science and Technology Osaka University
• 著者所属: Graduate School of Information Science and Technology Osaka University
• 著者所属: Graduate School of Information Science and Technology Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Information Science and Technology,Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Information Science and Technology,Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Information Science and Technology,Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Information Science and Technology,Osaka University
• 著者所属(英): en
• 著者所属(英): Graduate School of Information Science and Technology,Osaka University
• 著者名: Yoshiyuki, Kido; Shigeto, Seno; Susumu, Date; Yoichi, Takenaka; Hideo, Matsuda
• 著者名(英): Yoshiyuki, Kido; Shigeto, Seno; Susumu, Date; Yoichi, Takenaka; Hideo, Matsuda
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: The number of biological databases has been increasing rapidly as a result of progress in biotechnology. As the amount and heterogeneity of biological data increase it becomes more difficult to manage the data in a few centralized databases. Moreover the number of sites storing these databases is getting larger and the geographic distribution of these databases has become wider. In addition biological research tends to require a large amount of computational resources i.e. a large number of computing nodes. As such the computational demand has been increasing with the rapid progress of biological research. Thus the development of methods that enable computing nodes to use such widely-distributed database sites effectively is desired. In this paper we propose a method for providing data from the database sites to computing nodes. Since it is difficult to decide which program runs on a node and which data are requested as their inputs in advance we have introduced the notion of “data-staging” in the proposed method. Data-staging dynamically searches for the input data from the database sites and transfers the input data to the node where the program runs. We have developed a prototype system with data-staging using grid middleware. The effectiveness of the prototype system is demonstrated by measurement of the execution time of similarity search of several-hundred gene sequences against 527 prokaryotic genome data.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: The number of biological databases has been increasing rapidly as a result of progress in biotechnology. As the amount and heterogeneity of biological data increase, it becomes more difficult to manage the data in a few centralized databases. Moreover, the number of sites storing these databases is getting larger, and the geographic distribution of these databases has become wider. In addition, biological research tends to require a large amount of computational resources, i.e., a large number of computing nodes. As such, the computational demand has been increasing with the rapid progress of biological research. Thus, the development of methods that enable computing nodes to use such widely-distributed database sites effectively is desired. In this paper, we propose a method for providing data from the database sites to computing nodes. Since it is difficult to decide which program runs on a node and which data are requested as their inputs in advance, we have introduced the notion of “data-staging” in the proposed method. Data-staging dynamically searches for the input data from the database sites and transfers the input data to the node where the program runs. We have developed a prototype system with data-staging using grid middleware. The effectiveness of the prototype system is demonstrated by measurement of the execution time of similarity search of several-hundred gene sequences against 527 prokaryotic genome data.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12177013
• 書誌情報: IPSJ Transactions on Bioinformatics （TBIO）; 巻 49, 号 SIG5(TBIO4), p. 58-64, 発行日 2008-03-15
• ISSN / 収録物識別子タイプ: ISSN
• ISSN / 収録物識別子: 1882-6679
• 出版者 / 言語: ja
• 出版者: 情報処理学会