CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis

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• 作者：Kentaro Inoue (1)
  Kazuhiro Maeda (1)
  Takaaki Miyabe (1)
  Yu Matsuoka (1)
  Hiroyuki Kurata (1) (2)
  
• 关键词：Simulator ; Automatic modeling ; Global parameter optimization ; Robustness
• 刊名：Bioprocess and Biosystems Engineering
• 出版年：2014
• 出版时间：September 2014
• 年：2014
• 卷：37
• 期：9
• 页码：1925-1927
• 全文大小：163 KB
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• 作者单位：Kentaro Inoue (1)
  Kazuhiro Maeda (1)
  Takaaki Miyabe (1)
  Yu Matsuoka (1)
  Hiroyuki Kurata (1) (2)
  
  1. Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
  2. Biomedical Informatics R&D Center, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
  
• ISSN：1615-7605

文摘

Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.