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Development of network infostructure for multi-level modeling for neuroscience

Research Project

Project/Area Number 25730180
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionOkinawa Institute of Science and Technology Graduate University

Principal Investigator

ASAI Yoshiyuki  沖縄科学技術大学院大学, 統合オープンシステムユニット, グループリーダー (00415639)

Project Period (FY) 2013-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2013: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
Keywords多階層モデリング / インフォストラクチャ / 計算神経科学 / データベース / システム生理学 / モデルシェアリング
Outline of Final Research Achievements

In this work, during two years, we have developed an “infostructure” which can provide a total support to every aspect of a research cycle including model building, model/data store and share, executing simulations, and discussions based on those activities. The databases with additional functions to share data utilizing existing SNSs to accurate discussions based on the data in the database are opened at Physiome.jp (http://physiome.jp). Besides to support model building on neuroscience, we expanded a open software platform PhysioDesigner so that it can import models written in NeuroML.

Report

(3 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Research-status Report
  • Research Products

    (35 results)

All 2015 2014 2013 Other

All Journal Article (5 results) (of which Peer Reviewed: 3 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (21 results) (of which Invited: 3 results) Book (1 results) Remarks (7 results) Patent(Industrial Property Rights) (1 results) (of which Overseas: 1 results)

  • [Journal Article] Accelerating ODE-based Simulation of General and Heterogeneous Biophysical Models using a GPU2014

    • Author(s)
      Tomohiro Okuyama, Masao Okita, Takeshi Abe, Yoshiyuki Asai, Hiroaki Kitano, Taishin Nomura, and Kenichi Hagihara
    • Journal Title

      IEEE Transactions on Parallel and Distributed Systems

      Volume: 201(印刷中) Issue: 8 Pages: 1966-1975

    • DOI

      10.1109/tpds.2013.198

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation2014

    • Author(s)
      Asai Y, Abe T, Oka H, Okita M, Hagihara K, Ghosh S, Matsuoka Y, Kurachi Y, Nomura T, Kitano H
    • Journal Title

      Advanced Biomedical Engineering

      Volume: 3 Issue: 0 Pages: 50-58

    • DOI

      10.14326/abe.3.50

    • NAID

      130005001705

    • ISSN
      2187-5219
    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] システムバイオロジー研究のためのソフトウェア・プラットフォームの動向2014

    • Author(s)
      浅井義之,安部武志,松岡由希子,Samik Ghosh,北野宏明
    • Journal Title

      Drug Delivery System

      Volume: 29 (5) Pages: 386-396

    • NAID

      130004874238

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Physiome.jpにおけるモデルデータベースとモデリング・シミュレーションプラットフォームとの連携 (ミニ特集 国内外バイオデータベースの現状と展望)2014

    • Author(s)
      浅井義之,野村泰伸 ,北野宏明
    • Journal Title

      計測と制御

      Volume: 53 (5) Pages: 426-431

    • Related Report
      2014 Annual Research Report
  • [Journal Article] Modeling of rifampicin-induced CYP3A4 activation dynamics for the prediction of clinical drug-drug interactions from in vitro data2013

    • Author(s)
      Fumiyoshi Yamashita, Yukako Sasa, Shuya Yoshida, Akihiro Hisaka, Yoshiyuki Asai, Hiroaki Kitano, Mitsuru Hashida, Hiroshi Suzuki
    • Journal Title

      PLoS One

      Volume: 8(9) Issue: 9 Pages: 1-11

    • DOI

      10.1371/journal.pone.0070330

    • NAID

      120005343920

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] [ランチョンセミナー] PhysioDesignerによる生理機能の多階層モデリング2015

    • Author(s)
      浅井義之
    • Organizer
      第88回日本薬理学会年会
    • Place of Presentation
      愛知県名古屋市
    • Year and Date
      2015-03-18 – 2015-03-20
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A framework for simulation of neural network models driven by experimental spike timing data2014

    • Author(s)
      Yoshiyuki Asai, Hiroaki Kitano, Alessandro E.P. Villa
    • Organizer
      The 11th International Neural Coding Workshop
    • Place of Presentation
      Versailles Cedex, France
    • Year and Date
      2014-10-06 – 2014-10-10
    • Related Report
      2014 Annual Research Report
  • [Presentation] Development of multilevel neural network modeling integrating spike train data on PhysioDesigner2014

    • Author(s)
      Yoshiyuki Asai, Takeshi Abe, Li Li, Hideki Oka, Yoshihisa Kurachi, Hiroaki Kitano
    • Organizer
      INCF Japan Node International Workshop: Advances in Neuroinformatics 2014
    • Place of Presentation
      Wako, Japan
    • Year and Date
      2014-09-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Interoperability between multilevel modeling platform PhysioDesigner and databases in Physiome.jp and Dynamic Brain Platform through Garuda platform2014

    • Author(s)
      Yoshiyuki Asai, Ken Kuwae, Li Li, Hiroaki Kitano, Hiroaki Wagatsuma, Yoko Yamaguchi
    • Organizer
      Neuroinformatics 2014
    • Place of Presentation
      Leiden, Netherlands
    • Year and Date
      2014-08-25 – 2014-08-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] PhysioDesignerによる多階層生体機能モデリングサポート技術の進展2014

    • Author(s)
      浅井義之, 安部武志, 李俐, 岡秀樹, 倉智嘉久, 北野宏明
    • Organizer
      第53回日本生体医工学会大会
    • Place of Presentation
      宮城県仙台市
    • Year and Date
      2014-05-24 – 2014-05-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Physiome.jpのモデルデータベースならびにツール連携の開発2014

    • Author(s)
      浅井義之, 安部武志, 李俐, 岡秀樹, 野村泰伸, 北野宏明
    • Organizer
      第53回日本生体医工学会大会
    • Place of Presentation
      宮城県仙台市
    • Year and Date
      2014-05-24 – 2014-05-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] フィジオームを指向した階層的モデリング/シミュレーション基盤2014

    • Author(s)
      浅井義之,安部武志,北野宏明
    • Organizer
      日本薬剤学会第29年会
    • Place of Presentation
      埼玉県大宮市
    • Year and Date
      2014-05-20 – 2014-05-22
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Garuda Platform を介したDynamic Brain Platformとモデル開発・シミュレーション環境をつなぐ連携システム開発2014

    • Author(s)
      浅井義之, 桑江健, 北野宏明, 我妻広明, 山口陽子.
    • Organizer
      ニューロコンピューティング研究会
    • Place of Presentation
      九州工業大学 (福岡)
    • Related Report
      2013 Research-status Report
  • [Presentation] 腎臓の生理機能モデリング2014

    • Author(s)
      浅井義之, 北野宏明.
    • Organizer
      セミナー
    • Place of Presentation
      協和発酵キリン株式会社
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesigner の現状と今後2014

    • Author(s)
      浅井義之
    • Organizer
      第八回多階層生体機能学領域全体会議
    • Place of Presentation
      京都大学薬学部 (京都)
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Image based realistic EEG/MEG simulation in PhysioDesigner2013

    • Author(s)
      Hideki Oka, Ken-ichiro Iwasaki, Yoshiyuki Asai, Taishin Nomura, Yoko Yamaguchi.
    • Organizer
      Neuro2013
    • Place of Presentation
      Kyoto International Conference Center, Kyoto
    • Related Report
      2013 Research-status Report
  • [Presentation] Physiodesigner and Flint: Modeling and Simulation Tools for Multilevel Physiological Systems2013

    • Author(s)
      Yoshiyuki Asai
    • Organizer
      The 2nd HD-Physiology International Symposium 2013
    • Place of Presentation
      Marunouchi Plaza Hall, Tokyo
    • Related Report
      2013 Research-status Report
  • [Presentation] Flint K3: Cloud-based simulation service powered by Flint (poster)2013

    • Author(s)
      Yoshiyuki Asai, Takeshi Abe, Masao Okita, Tomohiro Okuyama, Ken-ichi Hagihara, Yoshihisa Kurachi, Hiroaki Kitano.
    • Organizer
      The 2nd HD-Physiology International Symposium 2013
    • Place of Presentation
      Marunouchi Plaza Hall, Tokyo
    • Related Report
      2013 Research-status Report
  • [Presentation] A versatile platform for multilevel modeling of physiological systems: Template/instance2013

    • Author(s)
      Yoshiyuki Asai, Takeshi Abe, Hideki Oka, Masao Okita, Tomohiro Okuyama, Ken-ichi Hagihara, Samik Ghosh, Yukiko Matsuoka, Yoshihisa Kurachi, Hrioaki Kitano.
    • Organizer
      IEEE EMBC2013
    • Place of Presentation
      Osaka International Convention Center, Osaka
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesigner for Multilevel Neural System Modeling2013

    • Author(s)
      Yoshiyuki Asai, Hideki Oka, Li Li, Takeshi Abe, Yoshihisa Kurachi and Hiroaki Kitano.
    • Organizer
      Neuroinformatics2013
    • Place of Presentation
      Karolinska Institutet, Sweden
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesigner and Flint with Garuda2013

    • Author(s)
      Takeshi Abe, Yoshiyuki Asai.
    • Organizer
      Garuda workshop in ICSB2013
    • Place of Presentation
      Copenhagen, Denmark
    • Related Report
      2013 Research-status Report
  • [Presentation] Multilevel modeling using SBML and PHML on PhysioDesigner (poster)2013

    • Author(s)
      Yoshiyuki Asai, Takeshi Abe, Hideki Oka, Yukiko Matsuoka, Ghosh Samik, Yoshihisa Kurachi, Hiroaki Kitano.
    • Organizer
      ICSB2013
    • Place of Presentation
      Copenhagen, Denmark
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesigner and Flint: a platform for multilevel modeling of physiological systems and simulation (poster)2013

    • Author(s)
      Asai, Yoshiyuki; Abe, Takeshi; Oka, Hideki; Okita, Masao; Okuyama, Tomohiro; Hagihara, Ken-ichi; Kurachi, Yoshihisa; Kitano, Hiroaki.
    • Organizer
      ICCB2013
    • Place of Presentation
      Leuven, Belgium
    • Related Report
      2013 Research-status Report
  • [Presentation] A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation (poster)2013

    • Author(s)
      Yoshiyuki Asai, Takeshi Abe, Hideki Oka, Masao Okita, Ken-ichi Hagihara, Samik Ghosh, Yukiko Matsuoka, Yoshihisa Kurachi, Taishin Nomura, Hiroaki Kitano.
    • Organizer
      生体医工学シンポジウム2013
    • Place of Presentation
      九州工業大学 (福岡)
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesignerを用いた生理機能モデリング2013

    • Author(s)
      浅井義之, 北野宏明.
    • Organizer
      セミナー
    • Place of Presentation
      田辺三菱製薬株式会社
    • Related Report
      2013 Research-status Report
  • [Presentation] PhysioDesignerを用いた生理機能モデリング2013

    • Author(s)
      浅井義之, 北野宏明.
    • Organizer
      セミナー
    • Place of Presentation
      協和発酵キリン株式会社
    • Related Report
      2013 Research-status Report
  • [Book] Toward an integrated software platform for systems pharmacology (Book title: Biopharmaceutics & Drug Disposition)2013

    • Author(s)
      Samik Ghosh; Yukiko Matsuoka; Yoshiyuki Asai; Kun-Yi Hsin; Hiroaki Kitano.
    • Publisher
      John Wiley & Sons, Ltd.
    • Related Report
      2013 Research-status Report
  • [Remarks] Physiome.jp

    • URL

      http://physiome.jp

    • Related Report
      2014 Annual Research Report
  • [Remarks] PhysioDesigner

    • URL

      http://physiodesigner.org

    • Related Report
      2014 Annual Research Report
  • [Remarks] Flint K3

    • URL

      http://flintk3.org

    • Related Report
      2014 Annual Research Report
  • [Remarks] PH Database

    • URL

      https://phdb.unit.oist.jp/modeldb/

    • Related Report
      2014 Annual Research Report
  • [Remarks] Physiome.jp

    • URL

      http://physiome.jp/

    • Related Report
      2013 Research-status Report
  • [Remarks] PhysioDesigner

    • URL

      http://physiodesigner.org/

    • Related Report
      2013 Research-status Report
  • [Remarks] Flint K3

    • URL

      http://flintk3.org

    • Related Report
      2013 Research-status Report
  • [Patent(Industrial Property Rights)] General-Purpose Simulation System Using Social Network Interface2013

    • Inventor(s)
      浅井義之 他5名
    • Industrial Property Rights Holder
      OIST, SBI
    • Industrial Property Rights Type
      特許
    • Filing Date
      2013-07-11
    • Related Report
      2013 Research-status Report
    • Overseas

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Published: 2014-07-25   Modified: 2019-07-29  

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