Editors: Kazuyuki Shimizu, Yu Matsuoka

Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism

eBook: US $99 Special Offer (PDF + Printed Copy): US $168
Printed Copy: US $119
Library License: US $396
ISBN: 978-1-68108-087-1 (Print)
ISBN: 978-1-68108-086-4 (Online)
Year of Publication: 2015
DOI: 10.2174/97816810808641150101


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 the influence of cell culture environment and the effect of knockout gene research when studying mutations that affect specific metabolic pathways. A systems biology approach, therefore, allows researchers to simulate experimental observations in order to predict outcomes at the cellular level.

Fundamentals of Systems Analysis and Modeling of Biosystems and Metabolism presents the basic concepts required for a systems biology approach towards cellular modeling. The book is intended as a primer for systems biology and biomedical engineering graduates and researchers. The text introduces readers to concepts related to cellular metabolism and its regulation, (enzymatic regulation and transcriptional regulation) which are also incorporated into a main metabolic model of a cell. The book also has chapters dedicated to identifying and incorporating steady-state and dynamic characteristics when considering a biological model for a computer simulation.

Readers will be able to (1) understand the basis of systems analysis towards creating appropriate biological models and simulations, (2) develop useful kinetic models based on cellular transport phenomena and metabolic regulation, (3) understand how to simulate a cell growth phenotype, and analyze it with experimental data.


The ultimate goal of systems biology is to reconstruct the cell system into the computer which can predict observable phenotypes. If this could be attained, the effects of culture environment and/or the specific genes knockout on the metabolism can be predicted without many exhaustive experiments, and thus more efficient metabolic engineering can be made. For this, it is quite important to understand the metabolic regulation mechanism and properly express it in the computer. Construction of a “virtual cell” will be an ambitious but realistic target that will provide significant benefits in the variety of practical applications from both scientific and metabolic engineering points of view.

The present book gives fundamentals of systems analysis and modeling as well as model identification, optimization and dynamics together with computer simulation toward the above ultimate goal. It is also critical to understand the metabolic regulation for the modeling, and thus some of the metabolic regulation of the main metabolism is also explained.

About the Authors

Prof. Kazuyuki Shimizu is based at the Kyushu Institute of Technology (KIT) and the Institute of Advanced Biosciences (IAB), Keio University, Japan. Following a BS and an MS in Chemical Engineering at Nagoya University, and a PhD in Chemical Engineering at Northwestern University, USA, he started his career in 1981 as a research associate at Nagoya University, Japan, and was promoted to associate professor in 1990. He then moved to the KIT as a professor in 1991. In 2000, he became an adjunct professor at IAB, Keio University, Japan. He has long been involved in research into 13C-metabolic flux analysis (13C–MFA), and studies on modeling and systems biology with the aim of gaining insight into the basic principles governing living cell systems. He recognizes the importance of uncovering the metabolic regulation mechanism of a cell system, based on both experimental (wet) and computational (dry) approaches. He has also organized a UK–Japan collaboration project on microbial systems biology toward developing virtual microbes by integration of the different levels of hierarchical omics information, such as transcriptomics, proteomics, metabolomics, and fluxomics data.

Dr.Yu Matsuoka is based at Kyushu Institute of Technology (KIT). Following a BS and PhD in Bioscience and Bioinformatics at KIT, she started her career in 2009 as a postdoctoral fellow at KIT. Her research interest is the systems biology, modeling, and computer simulation of a cell system.


Declared None.


The authors confirm that this ebook contents have no conflict of interest.

Keizo Watanabe
Tokyo Metropolitan University
E-mail: keizo@tmu.ac.jp


Yu Matsuoka
Kyushu Institute of Technology
Fukuoka 820-8502