Details of a Researcher - FUNAHASHI Akira

Papers - FUNAHASHI Akira

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ReCSiP: An FPGA-Based Biochemical Simulator

Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H

Electronics and Communications in Japan (Part II: Electronics) 90 ( 7 ) 1-10 2007.07

Research paper (scientific journal), Joint Work, Accepted

An integration of CellDesigner and SABIO-RK

FUNAHASHI Akira, JOURAKU Akiya, MATSUOKA Yukiko, KITANO Hiroaki

In Silico Biology 7 ( 2 ) S81-S90. 2007.03

Research paper (scientific journal), Joint Work, Accepted

FPGA-Based Stochastic Biochemical Simulator

Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H.

IPSJ Transactions on Advanced Computing System (Information Processing Society of Japan (IPSJ)) 48 ( SIG 3 (ACS 17) ) 45-58 - 58 2007.02

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

This paper discusses an FPGA implementation and evaluation of a Stochastic Simulation Algorithm (SSA) called the First Reaction Method. SSAs are widely known as rigorous methods for simulating the stochastic behaviors of various biochemical systems, but also as CPU-hogging applications due to vast repetition of the algorithm. This work accelerates the execution by achieving high throughput with concurrent simulations of highly utilized pipelined arithmetic units. For upgrading practical utility, the design stores intermediate data in a BlockRAM so that reconfiguration is unnecessary for different target biochemical systems. Benchmark results on an FPGA (Xilinx XC2VP70-5) have shown that the circuit provides throughput of approximately 83 times and 95 times compared to software execution on Xeon 2.80GHz when it was evaluated with biochemical models called TIS and D4S, respectively.

Integration of cell designer and SABIO-RK

Funahashi Akira, Jouraku Akiya, Matsuoka Yukiko, Kitano Hiroaki

In Silico Biology 7 ( SUPPL. 2 ) 81 - 90 2007

Research paper (scientific journal), Joint Work, Accepted, ISSN 1386-6338

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge for systems biology. To facilitate this research topic, we have developed CellDesigner to visualize, model and simulate biochemical networks. CellDesigner allows the users to easily create networks using solidly defined and comprehensive graphical notation. CellDesigner utilizes SBML to described models and can simulate models using an integrated SBML ODE Solver or third party simulation engine; thus enabling users to simulate through a sophisticated graphical user interface. Although CellDesigner can integrate with existing databases (KEGG, PubMed, BioModels, etc.), by calling a web browser, or connecting to its web page through HTTP, integration with SABIO-RK has the potential to expand connectivity and semi-automate visualization and model building. SABIO-RK contains information about biochemical reactions, related kinetic equations and parameters. Also information about the experimental conditions under which these parameters were measured is stored. By using the Web service API provided by the SABIO-RK team, we have succeeded to directly connect to the database, send search queries by ID or name of its component, and then import the query results into CellDesigner. © 2007 IOS Press. All rights reserved.

SBML models and MathSBML

Shapiro Bruce E., Finney Andrew, Hucka Michael, Bornstein Benjamin, Funahashi Akira, Jouraku Akiya, Keating Sarah M., Le Novère Nicolas, Matthews Joanne, Schilstra Maria J.

395 - 421 2007

MathSBML is an open-source, freely downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a tool-neutral, computer-readable format for representing models of biochemical reaction networks, and it is applicable to metabolic networks, cell signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, which is a standard medium for representing and transporting data that is widely supported on the Internet, as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication, and survival. In addition to Math- SBML, a number of other tools that support SBML model examination and manipulation are provided on the http://sbml.org Web site, including libSBML, which is a C/C++ library for reading SBML models; an SBML Toolbox for MATLAB; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica, as well as providing an API for model manipulation and simulation. © 2007 Humana Press Inc.

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Kinetics of dimension-restricted conditions

Hiroi Noriko, Funahashi Akira

Introduction to Systems Biology, 261-281 261 - 281 2007

Research paper (scientific journal), Joint Work, Accepted

The intracellular environment is crowded with skeletal proteins, organelle membranes, ribosomes, and so on. When molecular movement is restricted by such environments, some biochemical reaction processes cannot be represented by classical models, which assume that reactions occur in simple Newtonian fluids. Dimension-restricted reaction kinetics (DRRK) modeling is a method that can represent dimension-restricted reactions. We introduce the methods of DRRK in each case of reaction type. DRRK has another advantage in that it can be quantitatively evaluated by biochemical experiments. We also introduce the procedure of applying it for experimental results. This modeling method may provide the basis for in vivo-oriented modeling. © 2007 Humana Press Inc.

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

Nordling Torbjörn E M, Hiroi Noriko, Funahashi Akira, Kitano Hiroaki

Molecular BioSystems 3 ( 8 ) 523 - 529 2007

ISSN 1742-206X

Non-linear behaviour of biochemical networks, such as intracellular gene, protein or metabolic networks, is commonly represented using graphs of the underlying topology. Nodes represent abundance of molecules and edges interactions between pairs of molecules. These graphs are linear and thus based on an implicit linearization of the kinetic reactions in one or several dynamic modes of the total system. It is common to use data from different sources - experiments conducted under different conditions or even on different species - meaning that the graph will be a superposition of linearizations made in many different modes. The mixing of different modes makes it hard to identify functional modules, that is sub-systems that carry out a specific biological function, since the graph will contain many interactions that do not naturally occur at the same time. The ability to establish a boundary between the sub-system and its environment is critical in the definition of a module, contrary to a motif in which only internal interactions count. Identification of functional modules should therefore be done on graphs depicting the mode in which their function is carried out, i.e. graphs that only contain edges representing interactions active in the specific mode. In general, when an interaction between two molecules is established, one should always state the mode of the system in which it is active. This journal is © The Royal Society of Chemistry.

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CellDesigner

Funahashi Akira, Morohashi Mineo, Matsuoka Yukiko, Jouraku Akiya, Kitano Hiroaki

422 - 434 2007

Understanding the logic and dynamics of gene-regulatory and biochemical networks is a major challenge of systems biology. To facilitate this research topic, we have developed CellDesigner, a modeling tool of gene-regulatory and biochemical networks. CellDesigner supports users to easily create such networks, using solidly defined and comprehensive graphical representation (SBGN, systems biology graphical notation). CellDesigner is systems biology markup language (SBML) compliant, and has Systems Biology Workbench(SBW)-enabled software so that it can import/export SBML-described documents and integrate with other SBW-enabled simulation/analysis software packages. CellDesigner also supports simulation and parameter search, which is supported by integration with SBML ordinary differential equation (ODE) Solver, enabling us to simulate through our sophisticated graphical user interface. We can also browse and modify existing SBML models with references to existing databases. CellDesigner is implemented in Java; thus, it runs on various platforms such as Windows, Linux, and MacOS X. CellDesigner is freely available from our Web site at http://celldesigner.org/. © 2007 Humana Press Inc.

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Introduction to systems biology

S Choi

Humana press 2007

Research paper (scientific journal), Joint Work, Accepted

CellDesigner: a modeling tool for biochemical networks

Akira Funahashi, Yukiko Matsuoka, Akiya Jouraku, Hiroaki Kitano, Norihiro Kikuchi

Proceedings of the 38th conference on Winter simulation conference (WSC'06) (Winter Simulation Conference) 1707 - 1712 2006.12

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

Performance Evaluation of an Fpga-Based Biochemical Simulator ReCSip

Yasunori Osana, Masato Yoshimi, Yow Iwaoka, Toshinori Kojima, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Yuichiro Shibata, Naoki Iwanaga, N Kitano, Hideharu Amano

International Conference on Field Programmable Logic and Applications, 2006. FPL'06. (IEEE) 1 - 6 2006.08

Research paper (international conference proceedings), Joint Work, Accepted, ISSN 978-1-4244-0312-7

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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

International Conference on Field Programmable Logic and Applications, 2006. FPL'06. (IEEE) 1 - 6 2006.08

Research paper (international conference proceedings), Joint Work, Accepted, ISSN 978-1-4244-0312-7

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ReCSiP : An FPGA-Based General Purpose Biochemical Simulator

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

The IEICE transactions on information and systems (The Institute of Electronics, Information and Communication Engineers) 89 ( 6 ) 1163 - 1172 2006.06

Research paper (scientific journal), Joint Work, Accepted, ISSN 18804535

細胞内部の生化学反応を数理モデルとして記述し,シミュレーションを行うことで生命現象をシステムとして理解しようとする試みが盛んになっている.しかしながら,汎用のマイクロプロセッサで得られる処理能力は決して十分とはいえず,シミュレーションを高速に実行できる計算基盤が求められている.本論文では,FPGAを用いて常微分方程式を用いた生化学モデルのシミュレーションを高速に実行するシステムであるReCSiPの構成とハードウェアの実装について述べる.評価の結果,最大スループットはXilinx社のFPGAであるXC2VP70-5を用いて,Intel Pentium4 3.2GHzの50〜80倍のスループットを達成することができた.

ReCSiP: an FPGA-Based General Purpose Biochemical Simulator

Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H.

IEICE Transactions on Information and Systems J89-D ( 6 ) 1163-1172 - 10 2006.06

Research paper (scientific journal), Joint Work, Accepted, ISSN 8756-663X

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Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA.

Hiroi, N., Funahashi, A., and Kitano, H.

Cancer Gene Therapy (Nature Publishing Group) 13 ( 1 ) 7-12 - 12 2006.01

Research paper (scientific journal), Joint Work, Accepted, ISSN 0929-1903

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Analysis for Dimension-Restricted Kinetics with Bacterial Endonuclease Movement.

Hiroi, N., Funahashi, A., and Kitano, H.

WSEAS Transactions on Biology and Biomedicine 3 ( 1 ) 1-6 2006.01

Research paper (scientific journal), Joint Work, Accepted

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

IEEE International Conference on Field-Programmable Technology, 2005. (IEEE) 339 - 340 2005.12

Research paper (international conference proceedings), Joint Work, Accepted, ISSN 0-7803-9407-0

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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

International Conference on Field Programmable Logic and Applications, 2005. (IEEE) 2005 666 - 669 2005.08

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

A reconfigurable biochemical simulator by solving ordinary differential equations has received attention as a personal high speed environment for biochemical researchers. For efficient use of the reconfigurable hardware, static scheduling of high-throughput arithmetic pipeline structures is essential. This paper shows and compares some scheduling alternatives, and analyzes the tradeoffs between performance and hardware amount. Through the evaluation, it is shown that the sharing first scheduling reduces the hardware cost by 33.8% in average, with the up to 11.5% throughput degradation. Effects of sharing of rate law functions are also analyzed. © 2005 IEEE.

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A framework for ODE-based multimodel biochemical simulations on an FPGAs

Yasunori Osana, T Fukushima, M Yoshimi, Y Iwaoka, H Amano, A Funahashi, N Hiroi, H Kitano, Y Shibata, N Iwanaga

International Conference on Field Programmable Logic and Applications, 2005 (IEEE) 2005 574 - 577 2005.08

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

Today, mathematical modeling and simulation of biochemical pathways take a major role in biological researches. However, modern microprocessors cannot provide enough throughput to explore the large parameter space of target pathways. To address this problem, ReCSiP (a ReConfigurable Cell Simulation Platform), an FPGA-based biochemical simulator is proposed. It's an ODE-based simulator, which solves the rate-law functions. The framework proposed in this paper, enables to simulate pathways consisting many different types of chemical reactions by connecting the rate-law modules (solvers) on an FPGA. It provides the solver-to-solver communication mechanism on an FPGA and automatic configuration software to generate the circuit. © 2005 IEEE.

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An FPGA-based, multi-model simulation method for biochemical systems

Yasunori Osana, Tomonori Fukushima, Masato Yoshimi, Yow Iwaoka, A Funahashi, N Hiroi, Y Shibata, H Kitano, Hideharu Amano

Proceedings. 19th IEEE International Parallel and Distributed Processing Symposium, 2005. (IEEE) 2005 4 2005.04

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

Modeling and simulation of a cellular system on computers are now becoming an essential process in biological researches. However, modern PCs can't provide enough performance to simulate large-scale biochemical networks. ReCSiP is the alternative FPGA-based solution for biochemical simulations. In this paper, the novel method of biochemical simulation with multiple reaction models on an FPGA is proposed. The method generates optimal circuit and its optimal schedule for each simulation models written in SBML, the standard markup language in systems biology. ReCSiP has a Xilinx's XC2VP70 and achieved over 20-fold speedup compared to Intel's PentiumIII 1.13GHz.

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