E-CELL2 User's Manual


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The genome of a living organism is the whole set of its genes and can be regarded as the map of a life, but one cannot understand a life process exactly only by watching the map. A life is self-sustained with various chemical reactions cooperatively in the living body. Getting to know how pathways of biochemical reactions, such as metabolism and signal transduction, are constructed means mapping the map of a life phenomenon. Even if one can finish making a schematic of chemical-reaction networks in metabolism or signal transduction, there is much to be done unlock the secrets of life. In order to analyze how these complicated courses change dynamically, it is indispensable that chemical reactions are combined with each other, as building blocks of a model cell, which shows cellular dynamics by the simulation.

The E-CELL Simulation Environment enables you to simulate the entire cell. Without modeling various phenomena in the living body, such as metabolism, signal transduction and gene expression, the entire cell cannot be set as the object of a simulation approach. Therefore the software design must cover flexible modeling various biological phenomena inside a cell. There are three brunches of an open source project ( http://www.e-cell.org) for the E-CELL Simulation Environment. As for E-CELL1 and E-CELL3, Bioinformatics Laboratory at Keio University has mainly developed them. As for E-CELL2, which is introduced here, has been developed by the Bioinformatics Laboratory at Keio University and Mitsui Knowledge Industry Co., Ltd., setting one of the purposes of the project to offer the E-CELL Simulation Environment on MS-Windows. Now, let's build the environment on your PC to explore the world of E-CELL2!! E-CELL Simulation


Chapter 1 Installation
Chapter 2 Tutorial
Chapter 3 Basic Operation
Chapter 4 Creating Rule Files
Chapter 5 Creating User Defined Reactors
release note

E-CELL2 User's Manual
Last Update $Date: 2002/07/16 16:45:42 $.
Copyright: Keio University and Mitsui Knowledge Industry Co., Ltd. 2002