E-Cell System: Basic Concepts and Applications

Book Details

ISBN: 978-1-4614-6156-2
Pub Date: 14 Jan 2013
Pages: 194
Color Pages: 2
Figures: 65
Tables: 48

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E-Cell System: Basic Concepts and Applications

Satya Nanda Vel Arjunan
RIKEN Quantitative Biology Center
Suita, Osaka, Japan
Pawan K. Dhar
Centre for Systems and Synthetic Biology
University of Kerala
Kerala, India
Masaru Tomita
Institute for Advanced Biosciences
Keio University
Tsurroka, Yamagata, Japan

About this Book

Quantitative modeling has become an essential procedure toward understanding the cell at the systems level. Insights into the inner workings of biological networks can be obtained from mathematical analysis of biochemical models that might not be possible from direct experimentation alone. As one of advanced simulation platforms, the E-Cell System is of central relevance to the systems biology community. The E-Cell System, a multi-algorithm, multi-timescale object-oriented simulation platform, can be used to construct virtual biological systems. It permits the construction of model structure, such as gene regulatory and/or biochemical networks equivalent to a cell system or a part of the cell and perform both quantitative and qualitative analysis.

E-Cell System: Basic Concepts and Applications is a comprehensive reference (basics and applications) for the E-Cell System. The features and the inner workings of the software are written by the software developers themselves, while biological applications are described by systems biologists. The primary target audience for this book are biological research scientists interested in biochemical simulation and analysis. Others who may be interested include computer scientists or computational biologists concerned with the development of software for cell simulation or systems biology. The contents do not require any prior experience in modeling/simulation or skills in computer programming.

Table of Contents

PART 1. BASIC CONCEPTS

1. Introduction to Whole Cell Modeling
Pawan K. Dhar

2. Foundations of E-Cell Simulation Environment Architecture
Nathan Addy and Koichi Takahashi

3. Distributed Cell Biology Simulations with the E-Cell System
Masahiro Sugimoto

4. A Guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System
Satya Nanda Vel Arjunan

PART 2. APPLICATIONS

5. A Model Library of Bacterial Chemotaxis on E-Cell System
Yuri Matsuzaki

6. Electrophysiological Simulation of Developmental Changes in Action Potentials of Cardiomyocytes
Hitomi Itoh

7. Simulation of Human Erythrocyte Metabolism
Ayako Kinoshita

8. Dynamic Kinetic Modeling of Mitochondrial Energy Metabolism
Katsuyuki Yugi

9. A Computational Model of the Hepatic Lobule
Yasuhiro Naito

10. Decoding the Signaling Mechanism of Toll-Like Receptor 4 Pathways in Wild Type and Knockouts
Kumar Selvarajoo

11. Modeling of Hsp70-Mediated Protein Refolding
Bin Hu, Matthias P. Mayer and Masaru Tomita