Efficient Scheduling of Rate Law Functions for ODE-Based Multimodel Biochemical Simulation on an FPGA. - Naoki Iwanaga; Yuichiro Shibata; Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Tomonori Fukushima; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Hiroaki Kitano; Kiyoshi Oguri (FPL, 2005)

A Framework for ODE-Based Multimodel Biochemical Simulations on an FPGA. - Yasunori Osana; Yow Iwaoka; Tomonori Fukushima; Masato Yoshimi; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2005)

The Design of Scalable Stochastic Biochemical Simulator on FPGA. - Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPT, 2005)

An FPGA-Based, Multi-model Simulation Method for Biochemical Systems. - Yasunori Osana; Tomonori Fukushima; Masato Yoshimi; Yow Iwaoka; Yuichiro Shibata; Hiroaki Kitano; Akira Funahashi; Noriko Hiroi; Hideharu Amano (IPDPS, 2005)

Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip. - Yasunori Osana; Masato Yoshimi; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2006)

An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems. - Masato Yoshimi; Yasunori Osana; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hiroaki Kitano; Hideharu Amano (FPL, 2006)

A Combining technique of rate law functions for a cost-effective reconfigurable biological simulator. - Hideki Yamada; Naoki Iwanaga; Yuichiro Shibata; Yasunori Osana; Masato Yoshimi; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Hiroaki Kitano; et al. (FPL, 2007)

FPGA Implementation of a Data-Driven Stochastic Biochemical Simulator with the Next Reaction Method. - Masato Yoshimi; Yow Iwaoka; Yuri Nishikawa; Toshinori Kojima; Yasunori Osana; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Naoki Iwanaga; Hideki Yamada; Hiroaki Kitano; Hideharu Amano (FPL, 2007)

A Framework for Implementing a Network-Based Stochastic Biochemical Simulator on an FPGA. - Masato Yoshimi; Yuri Nishikawa; Toshinori Kojima; Yasunori Osana; Akira Funahashi; Noriko Hiroi; Yuichiro Shibata; Hideki Yamada; Hiroaki Kitano; Hideharu Amano (FPT, 2007)

Practical implementation of a network-based stochastic biochemical simulation system on an FPGA. - Masato Yoshimi; Yuri Nishikawa; Yasunori Osana; Akira Funahashi; Yuichiro Shibata; Hideki Yamada; Noriko Hiroi; Hiroaki Kitano; Hideharu Amano (FPL, 2008)

Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator. - Tomoya Ishimori; Hideki Yamada; Yuichiro Shibata; Yasunori Osana; Masato Yoshimi; Yuri Nishikawa; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Kiyoshi Oguri (ARC, 2009)

Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator. - Tomonori Ooya; Hideki Yamada; Tomoya Ishimori; Yuichiro Shibata; Yasunori Osana; Kiyoshi Oguri; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano (FPL, 2009)

A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA. - Hideki Yamada; Yasunori Osana; Tomoya Ishimori; Tomonori Ooya; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano; Yuichiro Shibata; Kiyoshi Oguri (ReConFig, 2009)

A datapath classification method for FPGA-based scientific application accelerator systems. - Yui Ogawa; Tomonori Ooya; Yasunori Osana; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano; Yuichiro Shibata; Kiyoshi Oguri (FPT, 2010)

Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator. - Hideki Yamada; Yui Ogawa; Tomonori Ooya; Tomoya Ishimori; Yasunori Osana; Masato Yoshimi; Yuri Nishikawa; Akira Funahashi; Noriko Hiroi; Hideharu Amano; Yuichiro Shibata; Kiyoshi Oguri (IPSJ Trans. Syst. LSI Des. Methodol., 2010)

From Microscopy Data to in silico Environments for in vivo Oriented Simulations. - Noriko Hiroi; Michael Klann; Keisuke Iba; Pablo de Heras Ciechomski; Shuji Yamashita; Akito Tabira; Takahiro Okuhara; Takeshi Kubojima; Yasunori Okada; Kotaro Oka; Robin Mange; Michael Unger; et al. (EURASIP J. Bioinform. Syst. Biol., 2012)

In vivo oriented modeling with consideration of intracellular crowding. - Noriko Hiroi; Keisuke Iba; Akito Tabira; Takahiro Okuhara; Takeshi Kubojima; Takumi Hiraiwa; Tetsuya J. Kobayashi; Kotaro Oka; Akira Funahashi (EMBC, 2013)

LibSBMLSim: a reference implementation of fully functional SBML simulator. - Hiromu Takizawa; Kazushige Nakamura; Akito Tabira; Yoichi Chikahara; Tatsuhiro Matsui; Noriko Hiroi; Akira Funahashi (Bioinform., 2013)

The systems biology simulation core algorithm. - Roland Keller; Alexander Dörr; Akito Tabira; Akira Funahashi; Michael J. Ziller; Richard R. Adams; Nicolas Rodriguez 001; Nicolas Le Novère; Noriko Hiroi; Hannes Planatscher; Andreas Zell; Andreas Dräger (BMC Syst. Biol., 2013)