Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism

Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism

Indexed in: EBSCO.

An understanding of biological systems at cellular and molecular levels helps researchers to model cellular behavior in different experimental conditions. This, in turn, can lead to insights about ...
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Background

Pp. 3-19 (17)

Kazuyuki Shimizu and Yu Matsuoka

Abstract

A brief overview is given for the current status of systems biology and modeling. Systems biology focuses on the profiling of the whole cellular metabolism using high-throughput data of different levels of information to understand and unraveling the underlying principles of the living organisms. The systems biology allows the development of mathematical models that can be computationally simulated. Various modeling approaches can be classified into two such as flux balance analysis (FBA) based on the stoichiometric constraints, and the kinetic modeling based on the enzymatic kinetic expressions. Although the former approach can be extended to large genome-scale, it is difficult to incorporate the metabolic regulation mechanism and to express the dynamics, while the latter approach can reasonable incorporate the metabolic regulation mechanism. The problem for the kinetic modeling is the increase in the model parameters as the system size becomes large. It is important for the modeling of a cell system to properly understand and express how the environmental stimuli are detected, how those are transduced, and how the cell metabolism is regulated. It is quite useful from science and metabolic engineering points of view to develop quantitative models toward whole cell modeling.

Keywords:

Virtual microbe, systems biology, flux balance analysis, genomescale, kinetic modeling, metabolic regulation, metabolic engineering.

Affiliation:

Institute of Advanced Biosciences Keio University Tsuruoka Yamagata 997-0017 Japan.