Development of network infostructure for multi-level modeling for neuroscience

• Project/Area Number: 25730180
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Okinawa 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: ¥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.

Research Products

• [Journal Article] Accelerating ODE-based Simulation of General and Heterogeneous Biophysical Models using a GPU (2014)
  • 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
  • Peer Reviewed
• [Journal Article] A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation (2014)
  • 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
  • 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
• [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
• [Journal Article] Modeling of rifampicin-induced CYP3A4 activation dynamics for the prediction of clinical drug-drug interactions from in vitro data (2013)
  • 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
  • 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
  • Invited
• [Presentation] A framework for simulation of neural network models driven by experimental spike timing data (2014)
  • 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
• [Presentation] Development of multilevel neural network modeling integrating spike train data on PhysioDesigner (2014)
  • 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
• [Presentation] Interoperability between multilevel modeling platform PhysioDesigner and databases in Physiome.jp and Dynamic Brain Platform through Garuda platform (2014)
  • 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
• [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
• [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
• [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
  • 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)
• [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
• [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)
  • Invited
• [Presentation] Image based realistic EEG/MEG simulation in PhysioDesigner (2013)
  • Author(s): Hideki Oka, Ken-ichiro Iwasaki, Yoshiyuki Asai, Taishin Nomura, Yoko Yamaguchi.
  • Organizer: Neuro2013
  • Place of Presentation: Kyoto International Conference Center, Kyoto
• [Presentation] Physiodesigner and Flint: Modeling and Simulation Tools for Multilevel Physiological Systems (2013)
  • Author(s): Yoshiyuki Asai
  • Organizer: The 2nd HD-Physiology International Symposium 2013
  • Place of Presentation: Marunouchi Plaza Hall, Tokyo
• [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
• [Presentation] A versatile platform for multilevel modeling of physiological systems: Template/instance (2013)
  • 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
• [Presentation] PhysioDesigner for Multilevel Neural System Modeling (2013)
  • Author(s): Yoshiyuki Asai, Hideki Oka, Li Li, Takeshi Abe, Yoshihisa Kurachi and Hiroaki Kitano.
  • Organizer: Neuroinformatics2013
  • Place of Presentation: Karolinska Institutet, Sweden
• [Presentation] PhysioDesigner and Flint with Garuda (2013)
  • Author(s): Takeshi Abe, Yoshiyuki Asai.
  • Organizer: Garuda workshop in ICSB2013
  • Place of Presentation: Copenhagen, Denmark
• [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
• [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
• [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)
• [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
• [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
• [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.
• [Remarks] Physiome.jp
  • URL: http://physiome.jp
• [Remarks] PhysioDesigner
  • URL: http://physiodesigner.org
• [Remarks] Flint K3
  • URL: http://flintk3.org
• [Remarks] PH Database
  • URL: https://phdb.unit.oist.jp/modeldb/
• [Remarks] Physiome.jp
  • URL: http://physiome.jp/
• [Remarks] PhysioDesigner
  • URL: http://physiodesigner.org/
• [Remarks] Flint K3
  • URL: http://flintk3.org
• [Patent(Industrial Property Rights)] General-Purpose Simulation System Using Social Network Interface (2013)
  • 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
  • Overseas