Pp. 3-19 (17)
Kazuyuki Shimizu and Yu Matsuoka
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.
Virtual microbe, systems biology, flux balance analysis, genomescale,
kinetic modeling, metabolic regulation, metabolic engineering.
Institute of Advanced Biosciences Keio University Tsuruoka Yamagata 997-0017 Japan.