[[ Journal Papers ]]
- 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.
- 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.
[[ Conference Papers ]]
[ 2006 ]
- Yow Iwaoka, et al.,
"An Acceleration
of a Biochemical Simulator on Programmable Hardware
(Poster)", The Seventh International Conference on
Systems Biology (ICSB2006). Yokohama,
Japan. 2006. PosterID: FI67.
- Yasunori Osana, et al., "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.
- Masato Yoshimi, et al., "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.
- Tomotaka Miyashiro, Akira Kitamura, Masato
Yoshimi, Hideharu Amano, Hironori Nakajyo & Noboru
Tanabe, "DIMMNET-2: A Reconfigurable Board Connected
into a Memory Slot". Proceedings of 2006
International Conference on Field Programmable Logic
and Applications, Madrid, Spain. Aug.2006.
- Daihan Wang, Hiroki Matsutani, Masato Yoshimi,
Hideharu Amano, & Michihiro Koibuchi, "A Parametric
Study of Scalable Interconnects on FPGAs", Paper
presented at the Proceedings of the 2006
International Conference on Engineering of
Reconfigurable Systems and Algorithms
(ERSA'06).
- Yuri Nishikawa, et al., "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.
[ 2005 ]
- Masato Yoshimi, et al.,
"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.
- Yasunori Osana, et al.,
"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.
- 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.
- Yasunori Osana, et al.,
"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.
[ 2004 ]
- Masato Yoshimi, et al., "Stochastic Simulation
for Biochemical Reactions on FPGA." The 14th
International Conference on Field Programmable Logic
and Applications. Antwerpen,
Belgium. Aug.2004. pp.105-114.
- Yasunori Osana, et al.,
"ReCSiP: a ReConfigurable Cell SImulation
Platform -Accelerating Biological Applications with
FPGA-." Proceedings of ASP-DAC '04. Yokohama,
Japan. Jan.2004. pp.731-733.
[ 2003 ]
- Yasunori Osana, et al.,
"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.
[[ Workshops ]]
[ 2006 ]
- Daihan Wang, Hiroki Matsutani, Masato Yoshimi,
Michihiro Koibuchi & Hideharu Amano,
"A Parametric Study of Packet-Swtched FPGA
Overlay Networks", IEICE.
RECONF2006-32, 2006.
- Masato Yoshimi, et al.,
"FPGA-based Stochastic Biochemical Simulator",
Proc. of Symposium on Advanced Computing Systems and
Infrastructures (SACSIS2006), May 2006.
- Toshinori Kojima, et al.,
"Implementation and Evaluation of
General-Purpose Host Interface on ReCSiP Board(in
Japanese)." IEICE. RECONF2006-10. May.2006.
- Yasunori Osana, et al.,
"Hardware-resource
Utilization Analysis on an FPGA-Based Biochemical
Simulator ReCSiP (in Japanese)."
IEICE. VLD2005-107. Jan.2006.
- Masato Yoshimi, et al.,
"Stochastic Biochemical Simulator with a
Data-transfer Network on an FPGA (in Japanese)."
IEICE. VLD2005-105. Jan.2006.
- Yuri Nishikawa, et al.,
"A Performance Improvement Strategy for
Numerical Integration on an FPGA-Based Biochemical
Simulator ReCSiP (in Japanese)."
IEICE. VLD2005-106. Jan.2006.
[ 2005 ]
- Yasunori Osana, et al., "A Feasibility Study on
Reconfigurable Multi-cellular System Simulator (in
Japanese)." IPSJ. ARC168. Nov.2005.
- Yasunori Osana: "CellDesigner-SBML Layout
Annotation Converter." The Tenth Workshop on Software
Platforms for Systems Biology, Boston, Massachusetts,
Oct. 2005.
- Yow Iwaoka, et al., "A System Design of
Accelerating Biochemical Simulations on Programmable
Hardware." The Tenth Workshop on Software Platforms
for Systems Biology, Boston, Massachusetts,
Oct. 2005.
- Yasunori Osana, et al., "The Control Mechanism of
an FPGA-Based Biochemical Simulator ReCSiP (in
Japanese)." IEICE. RECONF2005-39 Sep.2005.
- Yow Iwaoka, et al., "Building of the SBML System
for an FPGA-based Biochemical Simulator (In
Japanese)." IEICE. RECONF2005-40. Sep.2005.
- Masato Yoshimi, et al., "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.
- Yasunori Osana, et al.,
"Implementation and Evaluation of Numerical
Integrators on ReCSiP (In Japanese)."
IEICE. RECONF2005-7. May.2005.
- 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.
- Masato Yoshimi, et al., "Design of a Heap-tree
Based Scalable Stochastic Biochemical Simulator on an
FPGA (In Japanese)."
IEICE. RECONF2005-9. May.2005.
- Yasunori Osana, et al., "Design of the SBML
Processor for an FPGA-based Biochemical Simulator (In
Japanese)." IEICE. ARC161-3. Jan.2005.
- Yow Iwaoka, et al., "Design of Cellular Simulation
Platform for SBML Model (In Japanese)."
IPSJ. VLD2004-109. Jan.2005.
[ 2004 ]
- Yasunori Osana, et al., "Multi-Model Metabolic
Simulation of Cellular System on FPGAs (In Japanese)."
IEICE. CPSY/RECONF-4-8. Sep.2004.
- Masato Yoshimi, et al., "Acceleration Hardware of
Stochastic Simulation for Biochemical Reactions on
FPGA (In Japanese)."
IEICE. CPSY/RECONF-4-33. Sep.2004.
- Tomonori Fukushima, et al., "Acceleration Hardware
of Cell Lineage Construction System (in
Japanese)"
[ 2003 ]
- Yasunori Osana, et al., "Design of a Cell
Simulation System with FPGA (In Japanese)."
IEICE. CPSY2002-93. Jan.2003.
- Yasunori Osana, et al., "Metabolic simulation of
cellular system by FPGA-based system (In Japanese)."
IEICE. CPSY/RECONF-1-7. Sep.2003.
[ 2002 ]
- Yasunori Osana, et al., "Accelerate
Cell Simulators with Reconfigurable Hardware (In
Japanese)." IPSJ. ARC148-8. May.2002.