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

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Abstract

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.

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Acknowledgments

The authors thank Kenji Oohira (MTI Japan Inc.), who helped to develop the CADLIVE toolbox. This work was supported by Grant-in-Aid for Scientific Research (B) (25280107) from Japan Society for the Promotion of Science and Grant-in-Aid for Scientific Research on Innovative Areas (23134506) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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Correspondence to Hiroyuki Kurata.

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Supplementary material 1 (DOC 208 kb)

Supplementary material 2 (PDF 856 kb)

Supplementary Material 1 Overview of the CADLIVE.

Supplementary Material 2 Description for simulations and system analysis of example models

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Inoue, K., Maeda, K., Miyabe, T. et al. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis. Bioprocess Biosyst Eng 37, 1925–1927 (2014). https://doi.org/10.1007/s00449-014-1167-8

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  • DOI: https://doi.org/10.1007/s00449-014-1167-8

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