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A study of gene regulatory networks analysis on distributed and parallel computers using work steal method

Research Project

Project/Area Number 24700295
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Bioinformatics/Life informatics
Research InstitutionInstitute of Physical and Chemical Research (2013-2015)
Osaka University (2012)

Principal Investigator

Kido Yoshiyuki  国立研究開発法人理化学研究所, 生命システム研究センター, 客員研究員 (70506310)

Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywords分散コンピューティング / 遺伝子発現ネットワーク推定 / ジョブスケジューラ / 可視化 / 分散並列コンピューティング / スケジューリング / 遺伝子ネットワーク / ネットワーク推定 / 分散並列計算
Outline of Final Research Achievements

In this research, we have developed and implemented a job scheduler framework with work steal mechanism for large scale gene regulatory networks analysis. The analysis applications usually execute on a distributed and parallel computational environment. Because a whole of human genes is a approximate 20,000, therefore a human gene regulatory networks analysis needs large scale computational environment. So, our products aims to reduce a calculation time of gene regulatory networks analysis using work steal mechanism. A work steal mechanism is able to cut off a useless network estimation.
We also have modified and improved a network visualization application for large scale gene regulatory networks on a high resolution visualization system (i.e. tiled display wall).

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (11 results)

All 2016 2015 2014 2013 2012 Other

All Journal Article (3 results) (of which Peer Reviewed: 3 results,  Open Access: 1 results) Presentation (7 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Remarks (1 results)

  • [Journal Article] Research Note: A High Resolution Graph Viewer for Multi-monitor Visualization Environment2015

    • Author(s)
      Ryoichi Jingai, Yoshiyuki Kido, Susumu Date, Shinji Shimojo
    • Journal Title

      The Review of Socionetwork Strategy

      Volume: 9 Issue: 1 Pages: 19-27

    • DOI

      10.1007/s12626-015-0052-5

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Performance Characteristics of an SDN-enhanced Job Management System for Cluster Systems with Fat-tree Interconnect2014

    • Author(s)
      Yasuhiro Watashiba, Susumu Date, Hirotake Abe, Yoshiyuki Kido, Kohei Ichikawa, Hiroaki Yamanaka, Eiji Kawai, Shinji Shimojo, Haruo Takemura
    • Journal Title

      Proceedings of 6th IEEE International Conference on Cloud Computing Technology and Science (CloudCom2014)

      Volume: 0 Pages: 781-786

    • DOI

      10.1109/cloudcom.2014.82

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] 計算資源とネットワーク資源を考慮した割当ポリシを配備可能とするジョブ管理フレームワーク2014

    • Author(s)
      渡場康弘, 木戸善之, 伊達進, 阿部洋丈, 市川昊平, 山中広明, 河合栄治, 竹村治雄
    • Journal Title

      電子情報通信学会論文誌

      Volume: vol. J97-D, no. 6

    • NAID

      120006411135

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Presentation] Improvement of Scalability in Sharing Visualization Contents for Heterogeneous Display Environments2016

    • Author(s)
      Arata Endo, Yoshiyuki Kido, Susumu Date, Yasuhiro Watashiba, Kiyoshi Kiyokawa, Haruo Takemura, Shinji Shimojo
    • Organizer
      International Symposium on Grids & Clouds 2016 (ISGC2016)
    • Place of Presentation
      Academia Sinica, 台北市, 台湾
    • Year and Date
      2016-03-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] An Ontology-Based Model Search Extended to Deal with Accessibility Issues of Neuroinformatics Metadata with Multidirectional Attributes2015

    • Author(s)
      Yoshiyuki ASAI, Yoshiyuki KIDO, Kyota KAMIYOSHI, Taishin NOMURA, Hiroaki WAGATSUMA
    • Organizer
      INCF Japan Node International Workshop: Advances in Neuroinformatics 2015
    • Place of Presentation
      東京大学先端科学技術研究センター, 目黒区, 東京都
    • Year and Date
      2015-11-26
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 生命科学シミュレーションと大規模可視化2014

    • Author(s)
      木戸 善之
    • Organizer
      日本化学会情報化学部会 第二回若手の会
    • Place of Presentation
      化学会館, 東京
    • Year and Date
      2014-11-29
    • Related Report
      2014 Research-status Report
  • [Presentation] Prototyping and Evaluation of a Network-aware Job Management System on a Cluster System Leveraging OpenFlow2013

    • Author(s)
      Y. Watashiba, Y. Kido, S. Date, H. Abe, K. Ichikawa, H. Yamanaka, E. Kawai, H. Takemura
    • Organizer
      The 19th IEEE International Conference on Networks
    • Place of Presentation
      Singapore
    • Related Report
      2013 Research-status Report
  • [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data2012

    • Author(s)
      T. Yamanaka, Y. Kido, H. Daiyasu, S. Seno, Y. Takenaka, H. Matsuda
    • Organizer
      Genome Informatics 2012
    • Place of Presentation
      台南市国立成功大学(台湾)
    • Related Report
      2012 Research-status Report
  • [Presentation] 「京」を利用したインシリコ創薬基盤を目指して

    • Author(s)
      木戸善之
    • Organizer
      第35回情報化学討論会
    • Place of Presentation
      広島大学(広島県)
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 生命科学における「京」の必要性 ―「京」を用いた大規模遺伝子制御ネットワークの推定―

    • Author(s)
      木戸善之
    • Organizer
      第66回バイオメクフォーラム21研究会
    • Place of Presentation
      大阪大学(大阪府)
    • Related Report
      2012 Research-status Report
  • [Remarks]

    • URL

      http://handai.tk/~kido/

    • Related Report
      2015 Annual Research Report

URL: 

Published: 2013-05-31   Modified: 2019-07-29  

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