[Route 153]

Personal Information

Contact

Bioinformatics Lab., Dept. of Biosciences and Informatics, Faculty of Science and Technlogy, Keio University
3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan

E-Mail: osana@dna.bio.keio.ac.jp

Biography

Yasunori Osana received B.E., M.E. and Ph.D degree from Keio University in 2000, 2002 and 2005. He was a lecturer at Faculty of Technology, Tokyo University of Technology, Japan from April 2003 to March 2005, and also a lectuler at Faculty of Commerce, Chiba University of Commerce, Japan from April 2003 to March 2005. He is now a post doctral research fellow in Department of Biosciences and Informatics, Keio University, Japan from April 2005.

Research Projects

Publication

Journal Papers

  1. Yasunori Osana, Masato Yoshimi, You Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "An FPGA-Based Biochemical Simulator ReCSiP (In Japanese)." IEICE Trans. on Information and Systems. J89-D(6). Jun.2006. pp.1163-1172.
  2. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, and Hideharu Amano:
    "An FPGA-Based Acceleration Method for Metabolic Simulation." IEICE Trans. on Information and Systems. E87-D(8). Aug.2004. pp.2029-2037.
  3. Noriaki Suzuki, Katsunobu Nishimura, Tomonori Tamura, Yasunori Osana and Hideharu Amano:
    "Performance Evaluation of a Multicast Mechanism of RDT Network for a Massively Parallel Processor JUMP-1 (in Japanese)." IEICE Trans. on Information and Systems. J85-D1(12). Dec.2002. pp.1114-1125.

Conference Papers

    @Conference{OsanaWSC06 category = {workshop}, author = {Yasunori Osana and Masato Yoshimi and Yow Iwaoka and Toshinori Kojima and Yuri Nishikawa and Yuichiro Shibata and Naoki Iwanaga and Akira Funahashi and Noriko Hiroi and Hiroaki Kitano and Hideharu Amano}, title = {A Hardware Accelerator for Biochemical Simulations}, booktitle = {Winter Simulation Conference 2006}, year = {2006}, address = {}, month = {Dec.} } @Conference{YoshimiWSC06, category = {workshop}, author = {Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata and Naoki Iwanaga and Hiroaki Kitano and Hideharu Amano}, title = {Hardware Design of a Stochastic Biochemical Simulator}, booktitle = {Winter Simulation Conference 2006}, year = {2006}, address = {}, month = {Dec.} }
  1. Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "An Acceleration of a Biochemical Simulator on Programmable Hardware (Poster)", The Seventh International Conference on Systems Biology (ICSB2006). Yokohama, Japan. 2006. PosterID: FI67.
  2. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "Performance Evaluation of an FPGA-based Biochemical Simulator ReCSiP", Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. Aug.2006. 845-850.
  3. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shiabta, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems", Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. Aug.2006. 227-232.
  4. Yuri Nishikawa, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "An Evaluation and Investigation of Dual-Thread Numerical Integration Mechanism for FPGA-based Biochemical Simulator ReCSiP.", Proceedings of CoolChips IX. Yokohama, Japan. Apr.2006. 195-197.
  5. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "The Design of Scalable Stochastic Biochemical Simulator on FPGA.", Proceedings of 2005 IEEE International Conference on Field Programmable Technology. Signapore. Dec.2005. pp.339-340.
  6. Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA." Proccedings of the 15th Field Programmable Logic and its applications(FPL) 2005. Tampere, Finland. Aug.2005. pp.574-577.
  7. Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, and Kiyoshi Oguri:
    "Efficient Scheduling of Rate Law Functions for ODE-based Multimodel Biochemical Simulation on an FPGA." Proceedings of the 15th Field Programmable Logic and its applications(FPL) 2005. Tampere, Finland. Aug.2005. pp.666-669.
  8. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Hiroaki Kitano, and Hideharu Amano:
    "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems." Proceedings of the 19th International Parallel and Distributed Processing Symposium / Reconfigurable Architecture Workshop. Denver, Colorado, USA. Apr.2005.
  9. Masato Yoshimi, Yasunori Osana, Tomonori Fukushima, and Hideharu Amano:
    "Stochastic Simulation for Biochemical Reactions on FPGA." The 14th International Conference on Field Programmable Logic and Applications. Antwerpen, Belgium. Aug.2004. pp.105-114.
  10. Yasunori Osana, Tomonori Fukushima and Hideharu Amano:
    "ReCSiP: a ReConfigurable Cell SImulation Platform -Accelerating Biological Applications with FPGA-." Proceedings of ASP-DAC '04. Yokohama, Japan. Jan.2004. pp.731-733.
  11. Yasunori Osana, Tomonori Fukushima, and Hideharu Amano:
    "Implementation of ReCSiP: a Reconfigurable Cell SImulation Platform." The 13th International Conference on Field Programmable Logic and Applications. Lisbon, Portugal. Sep.2003. pp.766-775.
  12. Yasunori Osana, Hironori Nakajo, Noriaki Suzuki, Tomonori Tamura, and Hideharu Amano:
    "Performance Evaluation of a Parallel I/O Mechanism on a Massively Parallel Processing System JUMP-1." Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications Las Vegas, Nevada USA. Jun.2001. pp.1179-1185.

Workshops

  1. Toshinori Kojima, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano:
    "Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board(in Japanese)." IEICE. RECONF2006-10. May.2006.
  2. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. VLD2005-107. Jan.2006.
  3. Yuri Nishikawa, Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano : "A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. VLD2005-106. Jan.2006.
  4. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuri Nishikawa, Toshinori Kojima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano and Hideharu Amano, : "Stochastic Biochemical Simulator with a Data-transfer Network on an FPGA (in Japanese)." IEICE. VLD2005-105. Jan.2006.
  5. Yasunori Osana, Masato Yoshimi, and Hideharu Amano:
    "A Feasibility Study on Reconfigurable Multi-cellular System Simulator (in Japanese)." IPSJ. ARC168. Nov.2005.
  6. Yasunori Osana:
    "CellDesigner-SBML Layout Annotation Converter." The Tenth Workshop on Software Platforms for Systems Biology, Boston, Massachusetts, Oct. 2005.
  7. Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "A System Design of Accelerating Biochemical Simulations on Programmable Hardware." The Tenth Workshop on Software Platforms for Systems Biology, Boston, Massachusetts, Oct. 2005.
  8. Yasunori Osana, Yow Iwaoka, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "The Control Mechanism of an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. RECONF2005-39 Sep.2005.
  9. Yow Iwaoka, Yasunori Osana, Masato Yoshimi, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Building of the SBML System for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. RECONF2005-40. Sep.2005.
  10. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Yuichiro Shibata, Naoki Iwanaga, and Hideharu Amano:
    "Design of Floating-Point Arithmetic and Logic Units for Computational Science and Technology on FPGA (In Japanese)." PARTHENON Workshop. The 26th Meeting-1-7. May.2005.
  11. Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Implementation and Evaluation of Numerical Integrators on ReCSiP (In Japanese)." IEICE. RECONF2005-7. May.2005.
  12. Naoki Iwanaga, Yuichiro Shibata, Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Hiroaki Kitano, and Kiyoshi Oguri:
    "Scheduling of Rate Law Functions for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. RECONF2005-8. May.2005.
  13. Masato Yoshimi, Yasunori Osana, Yow Iwaoka, Tomonori Fukushima, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Design of a Heap-tree Based Scalable Stochastic Biochemical Simulator on an FPGA (In Japanese)." IEICE. RECONF2005-9. May.2005.
  14. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Design of the SBML Processor for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. ARC161-3. Jan.2005.
  15. Yow Iwaoka, Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, Hiroaki Kitano, and Hideharu Amano:
    "Design of Cellular Simulation Platform for SBML Model (In Japanese)." IPSJ. VLD2004-109. Jan.2005.
  16. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, and Hideharu Amano:
    "Multi-Model Metabolic Simulation of Cellular System on FPGAs (In Japanese)." IEICE. CPSY/RECONF-4-8. Sep.2004.
  17. Masato Yoshimi, Yasunori Osana, Tomonori Fukushima, and Hideharu Amano:
    "Acceleration Hardware of Stochastic Simulation for Biochemical Reactions on FPGA (In Japanese)." IEICE. CPSY/RECONF-4-33. Sep.2004.
  18. Tomonori Fukushima, Yasunori Osana, Tomonori Tamura, Shugo Hamahashi, Shuichi Onami and Hideharu Amano: "Acceleration Hardware of Cell Lineage Construction System (in Japanese)"
  19. Yasunori Osana, Tomonori Fukushima, and Hideharu Amano:
    "Design of a Cell Simulation System with FPGA (In Japanese)." IEICE. CPSY2002-93. Jan.2003.
  20. Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, and Hideharu Amano:
    "Metabolic simulation of cellular system by FPGA-based system (In Japanese)." IEICE. CPSY/RECONF-1-7. Sep.2003.
  21. Yasunori Osana, Ken-ichiro Anjo, and Hideharu Amano:
    "Accelerate Cell Simulators with Reconfigurable Hardware (In Japanese)." IPSJ. ARC148-8. May.2002.
  22. Masanori Nukata, Noriaki Suzuki, Hideharu Amano, Katsunobu Nishimura, Tomonori Tamura, Yasunori Osana, Masahito Konishi, Masahiro Goshima, and Shinji Tomita:
    "Performance Improvement by a Multicast Mechanism for a Massively Parallel Processor JUMP-1 (in Japanese)." IEICE. CPSY2001-49. Aug.2001.
  23. Yasunori Osana, Hironori Nakajo, Noriaki Suzuki, Tomonori Tamura, and Hideharu Amano:
    "Performance Evaluation of a Parallel I/O Mechanism of the Massively Parallel Processor JUMP-1 (in Japanese)." IEICE. CPSY2001-48. Aug.2001.
Yasunori Osana
Last modified at: