著書 - 舟橋　啓

数でとらえる細胞生物学

Ron Milo, Rob Phillips, 舟橋 啓, 羊土社, 2020年03月,  ページ数： 320

担当範囲: 監訳

機械学習を生命科学に使う! シークエンスや画像データをどう解析し、新たな生物学的発見につなげるか?

小林徹也, 杉村薫, 舟橋啓, 羊土社, 2020年12月,  ページ数： 240

担当範囲: 編集; 寄稿

機械学習を生命科学に使う! : シークエンスや画像データをどう解析し、新たな生物学的発見につなげるか?

小林 徹也, 杉村 薫, 舟橋 啓, 羊土社, 2020年

組織としての生命

荒金 直人, 堀田 耕司, 坂内健一,鳥海 崇, 山尾 佐智子, 舟橋 啓, 林 良信, 河野 礼子, 大宮 勘一郎, 黒沢 文貴, 田上 雅徳, 斎藤 慶典, 慶應義塾大学出版会, 2019年05月,  ページ数： 240

担当範囲: 生命現象を組織として理解する

バイオインフォマティクス入門

秋山 泰, 中井 謙太, 冨田 勝, 向井 有理, 長崎 英樹, 中村 保一, 池田 修己, 向井 友花, 越中谷 賢治, 飯田 泰広, 濱田 康太, 榊原 康文, 舟橋 啓, 鎌田 真由美, 小森 隆, 佐藤 健吾, 浜田 道昭, 内山 郁夫, 阿部 貴志, 野口 英樹, 白井 剛, 土方 敦司, 諏訪 牧子, 有田 正規, 後藤 修, 櫻井 望, 慶應義塾大学出版会, 2015年08月,  ページ数： 176

担当範囲: 第2章 計算科学

Modeling and Simulation Using CellDesigner

MATSUOKA Yukiko, FUNAHASHI Akira, GHOSH Samik, KITANO Hiroaki, Springer, 2014年06月

担当範囲: 121-145

　概要を見る

In silico modeling and simulation are effective means to understand how the regulatory systems function in life. In this chapter, we explain how to build a model and run the simulation using CellDesigner, adopting the standards such as SBML and SBGN.

Fabrication Method to A High Resolution Control in the Space of Cell Culturing Environment with Microfluidic System

Hiraiwa Takumi, Kimura Tadamasa, Takenaka Yuma, Tanamoto Ryo, Ota Hiroki, Kimura Hiroshi, Taguchi Yoshihiro, Miki Norihisa, Matsumoto Yoshinori, Oka Kotaro, Funahashi Akira, Hiroi Noriko, IEEE, 2014年01月

　概要を見る

This paper describes the fabrication and the evaluation of a reusable Cell Culturing Device, designed for a single cell and cellular networks analysis. This is the first success of combination of Microcontact Printing (mCP) and Vacuum Device. This combination has following advantages; (1) cells stay within the micropatterns for long enough duration to achieve local activation of cells or cellular networks (more than 24 h), (2) the displacement distance of laminar flow from the interface of two fluids in Cell Culturing Device keeps smaller than the diameter of a cell, (3) all components of our device except micropatterned substrate are reusable for further analyses. The success of the combination of above techniques provides a controllable environment for the local activation of a single cell and cellular networks. Our device allows to exhibit the different responses induced with the various conditions in a single observation sight at exactly the same time point.

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Introduction to Systems Biology

Shapiro, B., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S., Novere, N., Matthews, J., and Schilstra, M., Humana Press, 2007年07月

担当範囲: 395-421

Introduction to Systems Biology

FUNAHASHI Akira, Humana Press, 2007年07月

担当範囲: 422-434

Introduction to Systems Biology

Hiroi, N. and Funahashi, A., Humana Press, 2007年07月

担当範囲: 261-281

CellDesigner: A graphical biological network editor and workbench interfacing simulator

Funahashi, A. and Morohashi, M. and Matsuoka, Y. and Jouraku, A. and Kitano, H., Introduction to Systems Biology, 2007年

　概要を見る

<p>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 I

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Kinetics of dimension-restricted conditions

Hiroi, N. and Funahashi, A., 2007年

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SBML models and MathSBML

Shapiro, B.E. and Finney, A. and Hucka, M. and Bornstein, B. and Funahashi, A. and Jouraku, A. and Keating, S.M. and Le Novère, N. and Matthews, J. and Schilstra, M.J., 2007年

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Software Infrastructure for Effective Communication and Reuse of Computational Models

A Finney, M Hucka, BJ Bornstein, SM Keating, BE Shapiro, J Matthews, ..., 2006年03月

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System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Finney, A., Hucka, M., Bornstein, B., Keating, S., Shapiro, B., Matthews, J., Kovitz, B., Schilstra, M.,舟橋 啓, Doyle, J., 北野 宏明, MIT Press, 2006年03月

入門FreeBSD : Beginner's course

舟橋 啓, 西本 隆之助, 秀和システム, 1998年08月