Development of integrated software for metabolic flux analysis and its application

Abstract

The analysis of structure, pathway and flux distribution in metabolic networks has become an important approach for understanding the functionality of metabolic systems. For this analysis, a database system plays an important role in supporting convenient modeling of the metabolic systems. To provide it, a database system represents the characteristics of the biochemical networks. We designed a standardized and integrated scheme from the thorough comparison of the contents of different databases, and offered a “query by example”-type and navigational interface. It allows the user to find the data without background knowledge. Together with the database system, we developed the analysis software to facilitate integrated pathway and flux analysis for metabolic networks within a user-friendly graphical user interface. This package provides various desirable features like obtaining maximum theoretical yields, examining and comparing the influences of genetic modifications to the flux distributions, classifying the metabolic system with measurements according to the system determinacy, and supporting dynamic visualization of calculated fluxes mapped on metabolic pathways. To demonstrate the availability of developed package, it has been applied and tested for complex networks. In this study, we consider the metabolic analysis of Candida lipolytica producing citric acid carried out by Aiba and Matsuoka (1979) This package allows users who are not familiar with the mathematical background of the metabolic flux analysis to perform flux analysis of metabolic networks easily