E-Cell System: Basic Concepts
and Applications
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Satya Nanda Vel Arjunan
This book will be published in
December of 2008 |
About this bookQuantitative 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 aims to be a comprehensive reference (basics and applications) for the E-Cell System. The features and the inner workings of the software will be written by the software developers themselves, while biological applications will be described by systems biologists. The primary target audience for this book will be 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 will not require any prior experience in modeling/simulation or skills in computer programming. |
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Table of contentsPlanned List of Topics PART 1. BASIC CONCEPTS 1. Introduction to whole cell modeling 2. Foundations of E-Cell Simulation environment architecture 3. Distributed cell biology simulations with the E-Cell System 4. Simulation of biochemical reaction-diffusion in three-dimensional space PART 2. APPLICATIONS 5. Electrophysiological simulation of developmental changes in action potentials
6. Decoding the signaling mechanism of Toll-like receptor 4 pathways in wild type 7. Simulation of human erythrocyte metabolism 8. A model library of bacterial chemotaxis on E-Cell System 9. A computational model of hepatic lobule 10. Modeling of Hsp70-mediated protein refolding 11. Dynamic kinetic modeling of mitochondrial energy metabolism |
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