Papers - FUNAHASHI Akira

Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments

Noriko Hiroi, Takahiro Okuhara, Takeshi Kubojima, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Tetsuya J Kobayashi, Akira Funahashi

Frontiers in physiology (Frontiers Media SA)  3   293 2012.07

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1664-042X

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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, Akira Funahashi, Heinz Koeppl

EURASIP Journal on Bioinformatics and Systems Biology (Springer International Publishing AG)  2012 ( 1 ) 7 2012

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1687-4145

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BioPAX support in CellDesigner

Mi, Huaiyu, Muruganujan, Anushya, Demir, Emek, Matsuoka, Yukiko, Funahashi, Akira, Kitano, Hiroaki, Thomas, Paul D.

BIOINFORMATICS 27 ( 24 ) 3437 - 3438 2011.12

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1367-4803

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Physiological environment induces quick response–slow exhaustion reactions

Noriko Hiroi, James Lu, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Christoph Flamm, Kotaro Oka, Gottfried Köhler, Akira Funahashi

Frontiers in physiology (Frontiers Media SA)  2   50 2011.09

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1664-042X

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In vivo environments are highly crowded and inhomogeneous, which may affect reaction processes in cells. In this study we examined the effects of intracellular crowding and an inhomogeneity on the behavior of in vivo reactions by calculating the spectral dimension (d(s)), which can be translated into the reaction rate function. We compared estimates of anomaly parameters obtained from fluorescence correlation spectroscopy (FCS) data with fractal dimensions derived from transmission electron microscopy (TEM) image analysis. FCS analysis indicated that the anomalous property was linked to physiological structure. Subsequent TEM analysis provided an in vivo illustration; soluble molecules likely percolate between intracellular clusters, which are constructed in a self-organizing manner. We estimated a cytoplasmic spectral dimension d(s) to be 1.39 +/- 0.084. This result suggests that in vivo reactions initially run faster than the same reactions in a homogeneous space; this conclusion is consistent with the anomalous character indicated by FCS analysis. We further showed that these results were compatible with our Monte-Carlo simulation in which the anomalous behavior of mobile molecules correlates with the intracellular environment, leading to description as a percolation cluster, as demonstrated using TEM analysis. We confirmed by the simulation that the above-mentioned in vivo like properties are different from those of homogeneously concentrated environments. Additionally, simulation results indicated that crowding level of an environment might affect diffusion rate of reactant. Such knowledge of the spatial information enables us to construct realistic models for in vivo diffusion and reaction systems.

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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Lord Hendrix Barboza, Raoul JP Bonnal, Richard Bruskiewich, Jan C Bryne, José M Fernández, Akira Funahashi, Paul MK Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard Holland, Yoshinobu Kano, Edward A Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehvaslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwinski, Mark Schreiber, Martin Senger, Yasumasa Shigemoto, Daron M Standley, Hideaki Sugawara, Toshiyuki Tashiro, Oswaldo Trelles, Rutger A Vos, Mark D Wilkinson, William York, Christian M Zmasek, Kiyoshi Asai, Toshihisa Takagi

Journal of biomedical semantics (BioMed Central)  1 ( 1 ) 1 - 19 2010.12

Research paper (scientific journal), Joint Work, Accepted

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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

International Conference on Field-Programmable Technology (FPT) (IEEE)     441 - 444 2010.12

Research paper (international conference proceedings), Joint Work, Accepted

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Resource reduction design techniques play an important role to implement large-scale FPGA-based accelerator systems in floating point applications since available resources on FPGAs are limited. This paper proposes a dataflow graph classification method which makes groups of graphs based on their similarity in order to bring out efficient graph combining. Aiming at finding effective parameters for the k-means algorithm, various parameter combinations are evaluated and compared in terms of resource reduction effects and performance. The experimental results using an FPGA-based biochemical simulator reveal that the graph clustering that uses information on the maximum common subgraphs achieve 73.3% of resource reduction rate while alleviating the performance degradation. © 2010 IEEE.

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Design and Implementation of CellDesigner

FUNAHASHI Akira, MATSUOKA Yukiko, JOURAKU Akiya, TAKIZAWA Hiromu, HIROI Noriko, GHOSH Samik, KIKUCHI Norihiro, KITANO Hiroaki

Journal of The Society of Instrument and Control Engineers (The Society of Instrument and Control Engineers)  49 ( 8 ) 531 - 536 2010.08

Joint Work, Accepted,  ISSN  04534662

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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 Transactions on System LSI Design Methodology (一般社団法人 情報処理学会)  3 ( 3 ) 244 - 256 2010.08

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1882-6687

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For FPGA-based scientific simulation systems, hardware design technique that can reduce required amount of hardware resources is a key issue, since the size of simulation target is often limited by the size of the FPGA. Focusing on FPGA-based biochemical simulation, this paper proposes hardware design methodology which finds and combines common datapath for similar rate law functions appeared in simulation target models, so as to generate area-effective pipelined hardware modules. In addition, similarity-based clustering techniques of rate law functions are also presented in order to alleviate negative effects on performance for combined pipelines. Empirical evaluation with a practical biochemical model reveals that our method enables the simulation with 66% of the original hardware resources at a reasonable cost of 20% performance overhead.

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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

International Conference on Reconfigurable Computing and FPGAs, 2009. ReConFig'09. (IEEE)     125 - 130 2009.12

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  978-1-4244-5293-4

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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

International Conference on Field Programmable Logic and Applications, 2009. FPL 2009 (IEEE)     679 - 682 2009.08

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  1946-1488

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One of the obvious advantages of FPGA-based reconfigurable computing is customizability of a tradeoff point between performance and hardware costs. However, this tradeoff has rarely been discussed in a whole application level, which is the most important view for application users. This paper presents empirical evaluation of a hardware module sharing technique which can shift a tradeoff point of area and performance on an FPGA-based biochemical simulator. The biochemical simulation results are discussed in terms of hardware costs, simulation throughput, parallelism extracted in simulation hardware, and data transfer overheads.

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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

5th International Workshop, ARC 2009, Proceedings (Springer)  5453 ( 2009 ) 368 - 373 2009.03

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  978-3-642-00640-1

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High-throughput circuit design under device resource constraints is important for FPGA-based biochemical simulators. In this papers, we propose novel arithmetic pipeline scheduling techniques which effectively reduce hardware costs under given input bandwidth constraints. By assigning data-input timing based on an appropriate priority, arithmetic scheduling process is hardly affected by input bandwidth constraints. Evaluation results revealed that our method reduces hardware costs by 7.6% on average compared to the conventional ALAP scheduling.

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3P-239 Effect of molecular crowding on in vivo macromolecular reactions(Mathematical biology,The 47th Annual Meeting of the Biophysical Society of Japan)

Yashima Kenta, Hiroi Noriko, Funahashi Akira, Oka Kotaro

Seibutsu Butsuri (The Biophysical Society of Japan General Incorporated Association)  49 ( supplement ) S191 2009

Joint Work, Accepted,  ISSN  05824052

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Design and Evaluation of an FPGA-based Stochastic Biochemical Simulator for High-throughput Execution

YOSHIMI Masato, NISHIKAWA Yuri, OSANA Yasunori, FUNAHASHI Akira, HIROI Noriko, SHIBATA Yuuichirou, YAMADA Hideki, KITANO Hiroaki, AMANO Hideharu

IPSJ Transactions on Advanced Computing System (情報処理学会)  1 ( 3 ) 120-135 - 135 2008.12

Research paper (scientific journal), Joint Work, Accepted,  ISSN  1882-7829

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Stochastic biochemical simulation algorithms (SSAs) are generally known as exact methods to trace stochastic behaviors of target biochemical models. Due to vast amount of computation attributed to the nature of Monte Carlo Method, which SSAs are originated from, there is a strong urge for high-throughput execution environment. This paper proposes an FPGA implementation of a stochastic simulation system based on a computationally-efficient SSA called the Next Reaction Method, and studies the evaluation results of area and throughput in detail. The system conducts high-throughput multi-thread execution, using multiple thread modules accessing shared arithmetic and data modules. The network between modules are configurable, and supports flexible network structure according to target FPGAs. In order to evaluate the proposed design, the stochastic simulation system, which is capable of running 16 threads in parallel, was implemented on a middle-range FPGA. As the result of comparing the throughput in RTL simulation with software simulation run on Core 2 Quad Q6600, the system marked 4.2 times higher throughput using a real biochemical model called HSR. When several versions of virtually largescale models were tested on the same simulation environment, maximum of 5.4 times higher throughput was confirmed.

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

International Conference on Field Programmable Logic and Applications, 2008. FPL 2008 (IEEE)     663 - 666 2008.09

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  978-1-4244-1960-9

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FPGA上でのシミュレーションに向けた生化学コンパイラの実装

IWAOKA Yo, OSANA Yasunori, YOSHIMI Masato, NISHIKAWA Yuri, KOJIMA Toshinori, FUNAHASHI Akira, HIROI Noriko, SHIBATA Yuuichirou, IWANAGA Naoki, KITANO Hiroaki, AMANO Hideharu

電子情報通信学会論文誌 D J91-D ( 9 ) 2205-2216 2008.09

Research paper (scientific journal), Single Work, Accepted

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

FUNAHASHI Akira, MATSUOKA Yukiko, JOURAKU Akiya, MOROHASHI Mineo, KIKUCHI Norihiro, KITANO Hiroaki

IEEE Special Issue: Computational Systems Biology 96 ( 8 ) 1254-1265 - 1265 2008.08

Research paper (scientific journal), Joint Work, Accepted,  ISSN  0018-9219

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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

International Conference on Field-Programmable Technology, 2007. ICFPT 2007. (IEEE)     193 - 200 2007.12

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  978-1-4244-1471-0

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Deduction of intracellular sub-systems from a topological description of the network.

NORDLING Torbjorn, HIROI, Noriko, FUNAHASHI Akira and KITANO Hiroaki

Molecular Biosystems 3 ( 8 ) 523-529 2007.08

Research paper (scientific journal), Joint Work, Accepted

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, Kiyoshi Oguri

International Conference on Field Programmable Logic and Applications, 2007. FPL 2007 (IEEE)     808 - 811 2007.08

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  1946-1488

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In order to simulate large scale biological models with a reconfigurable FPGA-based biochemical simulator system, reduction of required resources are essential. This paper proposes a method which combines common terms in rate law functions appeared in biochemical models and generates a shared hardware module used for numerical integration. In this approach, two functions are combined in a tree structure level, followed by pipeline scheduling and arithmetic module binding. The evaluation result reveals that this approach reduces hardware resources by 31.4 % on average at the cost of 14.4 % throughput degradation.

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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

International Conference on Field Programmable Logic and Applications, 2007. FPL 2007 (IEEE)     254 - 259 2007.08

Research paper (international conference proceedings), Joint Work, Accepted,  ISSN  978-1-4244-1059-0