WinBEST-KIT for analyzing multilayer and multicellular systems

Tatsuya Sekiguchi, Masahiro Okamoto

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Previously, we developed a biochemical reaction simulator called WinBEST-KIT (Biochemical Engineering System analyzing Tool-KIT, which runs under Microsoft Windows) for analyzing complicated metabolic pathways. WinBEST-KIT provides an integrated simulation environment for experimental researchers in metabolic engineering. A particularly notable feature of WinBEST-KIT is that users can easily define and customize reaction symbols in the graphical user interface. Users can use their original kinetic equations, in addition to the pre-installed standard kinetic equations, to represent unknown kinetic mechanisms as reaction steps. However, owing to the increasing size of reaction systems to be analyzed in metabolic pathways, large-scale reaction systems must be divided into several arbitrary compartmental reaction systems and procedures are needed, such as multilayered hierarchical representation, to describe the interactions between the compartmental reaction systems. Accordingly, in this study, we developed a new version of WinBEST-KIT that enables users to construct several arbitrary reaction schemes as layers, to connect the layers, and to analyze the interactions between them. This hierarchical representation is effective for constructing multilayered mathematical models of biochemical systems, such as genome-enzyme-metabolite systems, reaction cascade systems, and multicellular systems.

Original languageEnglish
Title of host publication2011 IEEE International Conference on Systems Biology, ISB 2011
Pages161-166
Number of pages6
DOIs
Publication statusPublished - 2011
Event5th IEEE International Conference on Systems Biology, ISB 2011 - Zhuhai, China
Duration: Sep 2 2011Sep 4 2011

Other

Other5th IEEE International Conference on Systems Biology, ISB 2011
CountryChina
CityZhuhai
Period9/2/119/4/11

Fingerprint

Multilayers
Metabolic Networks and Pathways
Kinetics
Biochemical engineering
Metabolic engineering
Metabolic Engineering
Graphical user interfaces
Metabolites
Theoretical Models
Genes
Simulators
Research Personnel
Genome
Mathematical models
Enzymes

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Sekiguchi, T., & Okamoto, M. (2011). WinBEST-KIT for analyzing multilayer and multicellular systems. In 2011 IEEE International Conference on Systems Biology, ISB 2011 (pp. 161-166) https://doi.org/10.1109/ISB.2011.6033149

WinBEST-KIT for analyzing multilayer and multicellular systems. / Sekiguchi, Tatsuya; Okamoto, Masahiro.

2011 IEEE International Conference on Systems Biology, ISB 2011. 2011. p. 161-166.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sekiguchi, T & Okamoto, M 2011, WinBEST-KIT for analyzing multilayer and multicellular systems. in 2011 IEEE International Conference on Systems Biology, ISB 2011. pp. 161-166, 5th IEEE International Conference on Systems Biology, ISB 2011, Zhuhai, China, 9/2/11. https://doi.org/10.1109/ISB.2011.6033149
Sekiguchi T, Okamoto M. WinBEST-KIT for analyzing multilayer and multicellular systems. In 2011 IEEE International Conference on Systems Biology, ISB 2011. 2011. p. 161-166 https://doi.org/10.1109/ISB.2011.6033149
Sekiguchi, Tatsuya ; Okamoto, Masahiro. / WinBEST-KIT for analyzing multilayer and multicellular systems. 2011 IEEE International Conference on Systems Biology, ISB 2011. 2011. pp. 161-166
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