E-Cell System: Basic Concepts and Applications

✍ Scribed by Satya Nanda Vel Arjunan PhD, Pawan K. Dhar PhD, Masaru Tomita PhD (auth.)

• Publisher: Springer-Verlag New York
• Year: 2013
• Tongue: English
• Leaves: 185
• Series: Molecular Biology Intelligence Unit
• Edition: 1
• Category: Library

✦ Synopsis

The interdisciplinary field of molecular systems biology aims to understand the behavior and mechanisms of biological processes composed of individual molecular components. As we gain more qualitative and quantitative information of complex intracellular processes, biochemical modeling and simulation become indispensable not only to uncover the molecular mechanisms of the processes, but to perform useful predictions. To this end, the E‑Cell System, a multi‑algorithm, multi‑timescale object‑oriented simulation platform, can be used to construct predictive virtual biological systems. Gene regulatory and biochemical networks that constitute a sub‑ or a whole cellular system can be constructed using the E‑Cell System to perform qualitative and quantitative analyses. The purpose of E‑Cell System: Basic Concepts and Applications is to provide a comprehensive guide for the E‑Cell System version 3 in terms of the software features and its usage. While the publicly available E‑Cell Simulation Environment version 3 User's Manual provides the technical details of model building and scripting, it does not describe some of the underlying concepts of the E‑Cell System. The first part of the book addresses this issue by providing the basic concepts of modeling and simulation with the E‑Cell System.

✦ Table of Contents

Front Matter....Pages i-xiv
Front Matter....Pages 1-1
Introduction to Whole Cell Modeling....Pages 3-14
Foundations of E-Cell Simulation Environment Architecture....Pages 15-32
Distributed Cell Biology Simulations with the E-Cell System....Pages 33-41
A Guide to Modeling Reaction-Diffusion of Molecules with the E-Cell System....Pages 43-62
Front Matter....Pages 63-63
A Model Library of Bacterial Chemotaxis on E-Cell System....Pages 65-73
Electrophysiological Simulation of Developmental Changes in Action Potentials of Cardiomyocytes....Pages 75-88
Simulation of Human Erythrocyte Metabolism....Pages 89-104
Dynamic Kinetic Modeling of Mitochondrial Energy Metabolism....Pages 105-142
A Computational Model of the Hepatic Lobule....Pages 143-155
Decoding the Signaling Mechanism of Toll-Like Receptor 4 Pathways in Wild Type and Knockouts....Pages 157-167
Modeling of Hsp70-Mediated Protein Refolding....Pages 169-176
Back Matter....Pages 177-179

✦ Subjects

Molecular Medicine; Biomedicine general