Design and Implementation of high-performance spatial model simulator

• Project/Area Number: 24300112
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Keio University
• Principal Investigator: FUNAHASHI Akira 慶應義塾大学, 理工学部, 准教授 (70324548)
• Co-Investigator(Renkei-kenkyūsha): HIROI Noriko 慶應義塾大学, 理工学部・生命情報学科, 専任講師 (20548408)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000); Fiscal Year 2014: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2013: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2012: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
• Keywords: 情報工学 / 並列処理 / GPGPU / 空間モデル / 偏微分方程式 / 数値積分 / SBML / ハイパフォーマンス・コンピューティング / システムバイオロジー / 生体生命情報学 / バイオテクノロジー

Outline of Final Research Achievements

On a spatial model simulation based on PDEs, the simulation space is discretized by grid and simulators will compute on each grid sequentially which will increase the simulation time enormously depending on the number of grids. In order to solve this problem, we have applied parallelization of this sequential numerical integration on GPGPU (General Purpose computing on GPU).
In this research, we parallelized a CPU-based SBML spatial model simulator by GPGPU. We implemented numerical integration of advection, reaction and diffusion equation with NVIDIA CUDA. For the evaluation of the CPU application, we used Intel Xeon X5687 and for the evaluation of GPU case, we used Tesla K40. As a result, we achieved 52x performance improvement in advection equation, 64x in reaction equation, 63x in diffusion equation for 512x512 grids.

Research Products

• [Journal Article] High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes (2015)
  • Author(s): Yuichiro Nakai, Mitsunori Ozeki, Takumi Hiraiwa, Ryuichi Tanimoto, Akira Funahashi, Noriko Hiroi, Atsushi Taniguchi, Shigenori Nonaka, Viviane Boilot, Roshan Shrestha, Joanna Clark, Naoka Tamura, Viji M Draviam, Hiromasa Oku
  • Journal Title: Review of Scientific Instruments Volume: 86 Issue: 1 Pages: 013707-013707
  • DOI: 10.1063/1.4905330
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Acceleration of discrete stochastic biochemical simulation using GPGPU (2015)
  • Author(s): Kei Sumiyoshi, Kazuki Hirata, Noriko Hiroi, Akira Funahashi
  • Journal Title: Frontiers in physiology Volume: 6 Pages: 1-1
  • DOI: 10.3389/fphys.2015.00042
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The systems biology simulation core algorithm (2013)
  • Author(s): Keller, R., Dorr, A., Tabira, A., Funahashi, A., Ziller, M.J., Adams, R., Rodriguez, N., Le Novere, N., Hiroi, N., Planatscher, H., Zell, A. and Drager, A.
  • Journal Title: BMC Systems Biology Volume: 7 Issue: 1 Pages: 5-5
  • DOI: 10.1186/1752-0509-7-55
  • Peer Reviewed
• [Presentation] Computational Platform for Systems Biology (2014)
  • Author(s): Akira Funahashi
  • Organizer: Dagstuhl Seminar on Multiscale Spatial Computational Systems Biology
  • Place of Presentation: Wadern, Germany
  • Year and Date: 2014-11-23 – 2014-11-28
  • Invited
• [Presentation] CellDesigner (2014)
  • Author(s): Akira Funahashi, Noriko Hiroi
  • Organizer: Modelling and Simulation of Biological Models
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2014-09-14
• [Presentation] Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system. (2014)
  • Author(s): Hiraiwa, T., Kimura, T., Takenaka, Y., Tanamoto, R., Ota, H., Kimura, H., Taguchi, Y., Miki, N., Matsumoto, Y., Oka, K., Funahashi, A. and Hiroi, N.
  • Organizer: Micro Eloctro Mechanical Systems (MEMS)
  • Place of Presentation: San Francisco, USA
• [Presentation] Numerical Investigation for in vivo Oriented Modeling in 3D Crowded Space (2013)
  • Author(s): 久保島剛
  • Organizer: The 10th NIBB-EMBL Symposium 2013 Quantitative Bioimaging
  • Place of Presentation: 基礎生物学研究所・岡崎
  • Year and Date: 2013-03-17
• [Presentation] Understanding the characteristics of intracellular reaction space from the point of view of bio-molecular organization using spatial simulation (2013)
  • Author(s): 奥原嵩弘
  • Organizer: The 10th NIBB-EMBL Symposium 2013 Quantitative Bioimaging
  • Place of Presentation: 基礎生物学研究所・岡崎
  • Year and Date: 2013-03-17
• [Presentation] Physiological intracellular crowdedness is defined by the surface-to-volume ratio of sub-cellular compartments (2013)
  • Author(s): 広井賀子
  • Organizer: First Annual Winter Q-Bio Meeting
  • Place of Presentation: ハワイ・アメリカ
  • Year and Date: 2013-02-21
• [Presentation] Q-BioJP : Japanese Society for Quantitative Biology (2013)
  • Author(s): 舟橋啓
  • Organizer: First Annual Winter Q-Bio Meeting
  • Place of Presentation: ハワイ・アメリカ
  • Year and Date: 2013-02-20
• [Presentation] CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. (2013)
  • Author(s): Funahashi, A. and Hiroi, N.
  • Organizer: CellDesigner Workshop
  • Place of Presentation: Melbourne, Australia
  • Invited
• [Presentation] CellDesigner: A process diagram editor for gene-regulatory and biochemical networks (2013)
  • Author(s): Funahashi, A. and Hiroi, N.
  • Organizer: Computational and Mathematical Biology Course
  • Place of Presentation: Okinawa, Japan
  • Invited
• [Presentation] Setting up quantitative models in CellDesigner (2013)
  • Author(s): Funahashi, A. and Hiroi, N.
  • Organizer: Tutorials at international Conference on Systems Biology 2013 (ICSB2013)
  • Place of Presentation: Copenhagen, Denmark
• [Presentation] A neural differentiation model of pluripotent stem cells (2013)
  • Author(s): Takiguchi, R., Iwasaki, T., Hiraiwa, T., Kimura, T., Yamazaki, K., Funahashi, A. and Hiroi, N.
  • Organizer: International Conference on Systems Biology 2013 (ICSB2013)
  • Place of Presentation: Copenhagen, Denmark
• [Presentation] Development of microfluidic system for high resolution control of cell culturing environment (2013)
  • Author(s): Hiraiwa, T., Kimura, T., Tanamoto, R., Ota, H., Kimura, H., Taguchi, Y., Miki, N., Matsumoto, Y., Oka, K., Funahashi, A. and Hiroi, N.
  • Organizer: International Conference on Systems Biology 2013 (ICSB2013)
  • Place of Presentation: Copenhagen, Denmark
• [Presentation] Development of microfluidic system for high resolution control of long-term cell culturing environment (2013)
  • Author(s): Hiraiwa, T., Kimura, T., Tanamoto, R., Ota, H., Kimura, H., Taguchi, Y., Miki, N., Matsumoto, Y., Oka, K., Funahashi, A. and Hiroi, N.
  • Organizer: International Workshop on Quantitative Biology 2013
  • Place of Presentation: Osaka, Japan
• [Presentation] Design and Implementation of CellDesigner (2013)
  • Author(s): Funahashi, A., Matsuoka, Y., Ghosh, S., Hiroi, N. and Kitano, H.
  • Organizer: International Workshop on Quantitative Biology 2013
  • Place of Presentation: Osaka, Japan
• [Presentation] Development of High-speed 3D imaging system with electrically tunable lenses for deeper probing of subcellular structures (2013)
  • Author(s): Nakai, Y., Tamura, N., Hiraiwa, T., Okuhara, T., Draviam, V.M., Funahashi, A. and Hiroi, N.
  • Organizer: International Workshop on Quantitative Biology 2013
  • Place of Presentation: Osaka, Japan
• [Presentation] Implementation of a spatial model simulator and its SBML support (2012)
  • Author(s): 松井達広
  • Organizer: HARMONY2012
  • Place of Presentation: マーストリヒト・オランダ
  • Year and Date: 2012-05-24