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
- 2006- : MURASAKI: multiple-genome pattern detector
- 2001- : ReCSiP: an FPGA-based biochemical simulator
- 2000-2001 : JUMP-1: the massively parallel processing computer
Publication
Journal Papers
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"An FPGA-Based Biochemical Simulator ReCSiP (In Japanese)." IEICE Trans. on Information and Systems. J89-D(6). Jun.2006. pp.1163-1172. -
"An FPGA-Based Acceleration Method for Metabolic Simulation." IEICE Trans. on Information and Systems. E87-D(8). Aug.2004. pp.2029-2037. -
"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.}
}
-
"An Acceleration of a Biochemical Simulator on Programmable Hardware (Poster)", The Seventh International Conference on Systems Biology (ICSB2006). Yokohama, Japan. 2006. PosterID: FI67. -
"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. -
"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. -
"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. -
"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. -
"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. -
"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. -
"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. -
"Stochastic Simulation for Biochemical Reactions on FPGA." The 14th International Conference on Field Programmable Logic and Applications. Antwerpen, Belgium. Aug.2004. pp.105-114. -
"ReCSiP: a ReConfigurable Cell SImulation Platform -Accelerating Biological Applications with FPGA-." Proceedings of ASP-DAC '04. Yokohama, Japan. Jan.2004. pp.731-733. -
"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. -
"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
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"Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board(in Japanese)." IEICE. RECONF2006-10. May.2006. -
"Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. VLD2005-107. Jan.2006. - "A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. VLD2005-106. Jan.2006.
- "Stochastic Biochemical Simulator with a Data-transfer Network on an FPGA (in Japanese)." IEICE. VLD2005-105. Jan.2006.
-
"A Feasibility Study on Reconfigurable Multi-cellular System Simulator (in Japanese)." IPSJ. ARC168. Nov.2005. -
"CellDesigner-SBML Layout Annotation Converter." The Tenth Workshop on Software Platforms for Systems Biology, Boston, Massachusetts, Oct. 2005. -
"A System Design of Accelerating Biochemical Simulations on Programmable Hardware." The Tenth Workshop on Software Platforms for Systems Biology, Boston, Massachusetts, Oct. 2005. -
"The Control Mechanism of an FPGA-Based Biochemical Simulator ReCSiP (in Japanese)." IEICE. RECONF2005-39 Sep.2005. -
"Building of the SBML System for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. RECONF2005-40. Sep.2005. -
"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. -
"Implementation and Evaluation of Numerical Integrators on ReCSiP (In Japanese)." IEICE. RECONF2005-7. May.2005. -
"Scheduling of Rate Law Functions for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. RECONF2005-8. May.2005. -
"Design of a Heap-tree Based Scalable Stochastic Biochemical Simulator on an FPGA (In Japanese)." IEICE. RECONF2005-9. May.2005. -
"Design of the SBML Processor for an FPGA-based Biochemical Simulator (In Japanese)." IEICE. ARC161-3. Jan.2005. -
"Design of Cellular Simulation Platform for SBML Model (In Japanese)." IPSJ. VLD2004-109. Jan.2005. -
"Multi-Model Metabolic Simulation of Cellular System on FPGAs (In Japanese)." IEICE. CPSY/RECONF-4-8. Sep.2004. -
"Acceleration Hardware of Stochastic Simulation for Biochemical Reactions on FPGA (In Japanese)." IEICE. CPSY/RECONF-4-33. Sep.2004. - "Acceleration Hardware of Cell Lineage Construction System (in Japanese)"
-
"Design of a Cell Simulation System with FPGA (In Japanese)." IEICE. CPSY2002-93. Jan.2003. -
"Metabolic simulation of cellular system by FPGA-based system (In Japanese)." IEICE. CPSY/RECONF-1-7. Sep.2003. -
"Accelerate Cell Simulators with Reconfigurable Hardware (In Japanese)." IPSJ. ARC148-8. May.2002. -
"Performance Improvement by a Multicast Mechanism for a Massively Parallel Processor JUMP-1 (in Japanese)." IEICE. CPSY2001-49. Aug.2001. -
"Performance Evaluation of a Parallel I/O Mechanism of the Massively Parallel Processor JUMP-1 (in Japanese)." IEICE. CPSY2001-48. Aug.2001.