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 language | English |
|---|---|
| Title of host publication | 2011 IEEE International Conference on Systems Biology, ISB 2011 |
| Pages | 161-166 |
| Number of pages | 6 |
| DOIs | |
| Publication status | Published - 2011 |
| Event | 5th IEEE International Conference on Systems Biology, ISB 2011 - Zhuhai, China Duration: Sep 2 2011 → Sep 4 2011 |
Other
| Other | 5th IEEE International Conference on Systems Biology, ISB 2011 |
|---|---|
| Country | China |
| City | Zhuhai |
| Period | 9/2/11 → 9/4/11 |
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All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
Cite this
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 proceeding › Conference contribution
}
TY - GEN
T1 - WinBEST-KIT for analyzing multilayer and multicellular systems
AU - Sekiguchi, Tatsuya
AU - Okamoto, Masahiro
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=80054872791&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=80054872791&partnerID=8YFLogxK
U2 - 10.1109/ISB.2011.6033149
DO - 10.1109/ISB.2011.6033149
M3 - Conference contribution
AN - SCOPUS:80054872791
SN - 9781457716669
SP - 161
EP - 166
BT - 2011 IEEE International Conference on Systems Biology, ISB 2011
ER -