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Implementation of integrated biochemical network simulator

Research Project

Project/Area Number 21700328
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionKeio University

Principal Investigator

FUNAHASHI Akira  慶應義塾大学, 理工学部, 准教授 (70324548)

Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2009: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords生体生命システム情報学 / システムバイオロジー / 生化学ネットワーク / 生化学シミュレータ / 確率モデルシミュレーション / 生体生命情報学
Research Abstract

Understanding of the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed two simulation software packages. The one is a stochastic biochemical network simulator, and the other is a spatial model simulator. The spatial model simulator can solve set of partial differential equations, and thus can simulate reaction-diffusion systems. Our software packages will contribute to provide a computational platform for systems biology.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (40 results)

All 2012 2011 2010 2009 Other

All Journal Article (4 results) (of which Peer Reviewed: 4 results) Presentation (32 results) Remarks (4 results)

  • [Journal Article] 細胞シミュレータCell Designerの設計と実装2010

    • Author(s)
      舟橋啓、松岡由希子、上樂明也、瀧沢大夢、広井賀子、Samik Ghosh, 菊池紀広、北野宏明
    • Journal Title

      計測と制御

      Volume: Vol.49、No.8 Pages: 531-536

    • NAID

      10026585798

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] 細胞シミュレータCellDesignerの設計と実装2010

    • Author(s)
      舟橋啓
    • Journal Title

      計測と制御

      Volume: 49 Pages: 531-536

    • NAID

      10026585798

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The Systems Biology Graphical Notation2009

    • Author(s)
      Novere, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S. E., Calzone, L., Courtot,M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., and Kitano, H.
    • Journal Title

      Nature Biotechnology

      Volume: Vol.27, No.8 Pages: 734-741

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] The Systems Biology Graphical Notation2009

    • Author(s)
      Le Novere, N.
    • Journal Title

      Nature Biotechnology 27

      Pages: 735-741

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] 生化学ネットワーク解析環境CellDesignerの設計と実装2012

    • Author(s)
      舟橋啓
    • Organizer
      定量生物学の会第4回年会
    • Place of Presentation
      名古屋大学野依記念学術交流館
    • Year and Date
      2012-01-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] 定量生物に効く数値計算2012

    • Author(s)
      舟橋啓
    • Organizer
      定量生物学の会第4回年会
    • Place of Presentation
      名古屋大学野依記念学術交流館
    • Year and Date
      2012-01-07
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] An interactive equation based model builder2011

    • Author(s)
      A. Funahashi
    • Organizer
      Garuda 6
    • Place of Presentation
      Luxembourg
    • Year and Date
      2011-09-29
    • Related Report
      2011 Final Research Report
  • [Presentation] An interactive equation-based model builder2011

    • Author(s)
      Akira Funahashi
    • Organizer
      Garuda 6
    • Place of Presentation
      Esch-sur-Alzette, Luxembourg(招待講演)
    • Year and Date
      2011-09-29
    • Related Report
      2011 Annual Research Report
  • [Presentation] An interactive equation based model builder2011

    • Author(s)
      A. Funahashi
    • Organizer
      The Computational Modeling in Biology Network(COMBINE 2011)
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-09-04
    • Related Report
      2011 Final Research Report
  • [Presentation] Implementation of spatial simulator and its SBML support2011

    • Author(s)
      A. Funahashi
    • Organizer
      The Computational Modeling in Biology Network(COMBINE 2012)
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-09-04
    • Related Report
      2011 Final Research Report
  • [Presentation] Implementation of spatial simulator and its SBML support2011

    • Author(s)
      Akira Funahashi
    • Organizer
      The Computational Modeling in Biology Network (COMBINE) 2011
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-09-04
    • Related Report
      2011 Annual Research Report
  • [Presentation] An interactive equation-based model builder2011

    • Author(s)
      Akira Funahashi
    • Organizer
      The Computational Modeling in Biology Network (COMBINE) 2011
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-09-04
    • Related Report
      2011 Annual Research Report
  • [Presentation] CellDesigner : A Process Diagram Editor for Gene-Regulatory and Biochemical Networks2011

    • Author(s)
      A. Funahashi
    • Organizer
      12^<th> International Conference on Systems Biology(ICSB 2011)
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-08-28
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner : A Process Diagram Editor for Gene-Regulatory and Biochemical Networks2011

    • Author(s)
      Akira Funahashi
    • Organizer
      12^<th> International Conference on Systems Biology (ICSB 2011)
    • Place of Presentation
      Heidelberg, Germany
    • Year and Date
      2011-08-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] CellDesigner2011

    • Author(s)
      A. Funahashi
    • Organizer
      FEBS SystemsX Sysbio2010
    • Place of Presentation
      Innsbruck, Austria
    • Year and Date
      2011-02-27
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner2011

    • Author(s)
      Funahashi, A.
    • Organizer
      FEBS SystemsX SysBio2010
    • Place of Presentation
      オーストリア・インスブルック
    • Year and Date
      2011-02-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] CellDesigner2011

    • Author(s)
      A. Funahashi
    • Organizer
      Garuda 4 workshop
    • Place of Presentation
      沖縄科学技術研究基盤整備機構
    • Year and Date
      2011-02-24
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner Plugin2011

    • Author(s)
      Funahashi, A.
    • Organizer
      Garuda 4 workshop
    • Place of Presentation
      沖縄・沖縄科学技術研究基盤整備機構
    • Year and Date
      2011-02-24
    • Related Report
      2010 Annual Research Report
  • [Presentation] CellDesigner Plugin2011

    • Author(s)
      A. Funahashi
    • Organizer
      Garuda 4 workshop
    • Place of Presentation
      沖縄科学技術研究基盤整備機構
    • Year and Date
      2011-02-23
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner2011

    • Author(s)
      Funahashi, A.
    • Organizer
      Garuda 4 workshop
    • Place of Presentation
      沖縄・沖縄科学技術研究基盤整備機構
    • Year and Date
      2011-02-23
    • Related Report
      2010 Annual Research Report
  • [Presentation] 生化学ネットワーク解析環境CellDesignerの設計と実装2010

    • Author(s)
      舟橋啓
    • Organizer
      定量生物学の会 第3回年会
    • Place of Presentation
      東京大学生産技術研究所
    • Year and Date
      2010-11-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] CellDesigner4. 1 : A Process Diagram Editor for Gene-Regulatory and Biochemical Networks2010

    • Author(s)
      A. Funahashi
    • Organizer
      11^<th> International Conference on Systems Biology(ICSB 2010)
    • Place of Presentation
      Edinburgh, UK
    • Year and Date
      2010-10-10
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner4.1 : A Process Diagram Editor for Gene Regulatory and Biochemical Networks2010

    • Author(s)
      Funahashi, A.
    • Organizer
      11^<th> International Conference on Systems Biology
    • Place of Presentation
      イギリス・エジンバラ
    • Year and Date
      2010-10-10
    • Related Report
      2010 Annual Research Report
  • [Presentation] CellDesigner Plugin2010

    • Author(s)
      A. Funahashi
    • Organizer
      Garuda One workshop
    • Place of Presentation
      沖縄科学技術研究基盤整備機構
    • Year and Date
      2010-02-23
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner2010

    • Author(s)
      A. Funahashi
    • Organizer
      Garuda One workshop
    • Place of Presentation
      沖縄科学技術研究基盤整備機構
    • Year and Date
      2010-02-23
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner2010

    • Author(s)
      Funahashi, A.
    • Organizer
      Garuda One
    • Place of Presentation
      沖縄・沖縄科学技術研究基盤整備機構
    • Year and Date
      2010-02-23
    • Related Report
      2009 Annual Research Report
  • [Presentation] CellDesigner plugin2010

    • Author(s)
      Funahashi, A.
    • Organizer
      Garuda One
    • Place of Presentation
      沖縄・沖縄科学技術研究基盤整備機構
    • Year and Date
      2010-02-23
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生化学ネットワーク解析環境CellDesignerの設計と実装2010

    • Author(s)
      舟橋啓
    • Organizer
      定量生物学の会第2回年会
    • Place of Presentation
      大阪・大阪大学
    • Year and Date
      2010-01-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] CellDesigner2009

    • Author(s)
      A. Funahashi
    • Organizer
      Winter School on Computational Modeling in Biology
    • Place of Presentation
      沖縄科学技術研究基盤整備機構
    • Year and Date
      2009-12-17
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner2009

    • Author(s)
      Funahashi, A.
    • Organizer
      Winter School on Computational Modeling in Biology
    • Place of Presentation
      沖縄・沖縄科学技術研究基盤整備機構
    • Year and Date
      2009-12-17
    • Related Report
      2009 Annual Research Report
  • [Presentation] 生化学ネットワーク解析環境CellDesignerの設計と実装2009

    • Author(s)
      舟橋啓
    • Organizer
      第24回生体・生理工学シンポジウム
    • Place of Presentation
      東北大学
    • Year and Date
      2009-09-25
    • Related Report
      2011 Final Research Report
  • [Presentation] 生化学ネットワーク解析環境CellDesignerの設計と実装2009

    • Author(s)
      舟橋啓
    • Organizer
      第24回生体・生理工学シンポジウム
    • Place of Presentation
      仙台・東北大学
    • Year and Date
      2009-09-25
    • Related Report
      2009 Annual Research Report
  • [Presentation] CellDesigner4. 1β2009

    • Author(s)
      A. Funahashi
    • Organizer
      The 14^<th> SBML Forum Meeting
    • Place of Presentation
      Stanford, USA
    • Year and Date
      2009-09-03
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner4.12009

    • Author(s)
      Funahashi, A.
    • Organizer
      The 14^<th> SBML Forum Meeting
    • Place of Presentation
      米国・スタンフォード大学
    • Year and Date
      2009-09-03
    • Related Report
      2009 Annual Research Report
  • [Presentation] CellDesigner4. 1 : A Process Diagram Editor for Gene-Regulatory and Biochemical Networks2009

    • Author(s)
      A. Funahashi
    • Organizer
      10^<th> International Conference on Systems Biology(ICSB 2009)
    • Place of Presentation
      Stanford, USA
    • Year and Date
      2009-08-30
    • Related Report
      2011 Final Research Report
  • [Presentation] CellDesigner4.1 : A Process Diagram Editor for Gene Regulatory and Biochemical Networks2009

    • Author(s)
      Funahashi, A.
    • Organizer
      10^<th> International Conference on Systems Biology
    • Place of Presentation
      米国・スタンフォード大学
    • Year and Date
      2009-08-30
    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://celldesigner.org/

    • Related Report
      2011 Final Research Report
  • [Remarks]

    • URL

      http://celldesigner.org/

    • Related Report
      2011 Annual Research Report
  • [Remarks]

    • URL

      http://celldesigner.org/

    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://celldesigller.org/

    • Related Report
      2009 Annual Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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