A Distributed-Processing System for Accelerating Biological Research Using Data-Staging
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- Kido Yoshiyuki
- Graduate School of Information Science and Technology, Osaka University
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- Seno Shigeto
- Graduate School of Information Science and Technology, Osaka University
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- Date Susumu
- Graduate School of Information Science and Technology, Osaka University
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- Takenaka Yoichi
- Graduate School of Information Science and Technology, Osaka University
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- Matsuda Hideo
- Graduate School of Information Science and Technology, Osaka University
抄録
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.
収録刊行物
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- IPSJ Digital Courier
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IPSJ Digital Courier 4 250-256, 2008
一般社団法人 情報処理学会
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詳細情報 詳細情報について
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- CRID
- 1390282680200359680
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- NII論文ID
- 130000022196
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- ISSN
- 13497456
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- 本文言語コード
- en
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- データソース種別
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- JaLC
- Crossref
- CiNii Articles
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- 抄録ライセンスフラグ
- 使用不可