WINBEST-kit: Biochemical reaction simulator for analyzing multi-layered metabolic pathways

Tatsuya Sekiguchi, Hiroyuki Hamada, Masahiro Okamoto

研究成果: Contribution to journalArticle査読

抄録

We previously developed the biochemical reaction simulator WinBEST-KIT. In recent years, research interest has shifted from analysis of individual biochemical reactions to analysis of metabolic pathways as systems. These large-scale and complicated metabolic pathways can be considered as characteristic multi-layered structures, which, for convenience, are separated from whole biological systems according to their specific roles. These pathways include reactants having the same name but with unique stoichiometric coefficients arranged across many different places and connected between arbitrary layers. Accordingly, in this study, we have developed a new version ofWinBEST-KIT that allows users (1) to utilize shortcut symbols that can be arranged with multiple reactants having the same name but with unique stoichiometric coefficients, thereby providing a layout that is similar to metabolic pathways depicted in biochemical textbooks; (2) to create layers that divide large-scale and complicated metabolic pathways according to their specific roles; (3) to connect the layers by using shortcut symbols; and (4) to analyze the interactions between these layers. These new and existing features allow users to create and analyze such multi-layered metabolic pathways efficiently. Furthermore, WinBEST-KIT supports SBML, making it possible for users to utilize these new and existing features to create and publish SBML models.

本文言語英語
論文番号114
ジャーナルBioengineering
8
8
DOI
出版ステータス出版済み - 8 2021

All Science Journal Classification (ASJC) codes

  • バイオエンジニアリング

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