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E-Cell: Computer Simulation of the Cell

  1. Pawan Dhar1,
  2. Kouichi Takahashi2,
  3. Yoichi Nakayama2,
  4. Masaru Tomita2

Published Online: 15 SEP 2006

DOI: 10.1002/3527600906.mcb.200300061

Encyclopedia of Molecular Cell Biology and Molecular Medicine

Encyclopedia of Molecular Cell Biology and Molecular Medicine

How to Cite

Dhar, P., Takahashi, K., Nakayama, Y. and Tomita, M. 2006. E-Cell: Computer Simulation of the Cell. Encyclopedia of Molecular Cell Biology and Molecular Medicine. .

Author Information

  1. 1

    Bioinformatics Institute, Singapore

  2. 2

    Keio University, Tsuruoka, Japan

Publication History

  1. Published Online: 15 SEP 2006

This is not the most recent version of the article. View current version (15 MAR 2012)


Cells perform complex tasks with sheer simplicity. They are remarkable, tiny factories where thousands of jobs are performed in parallel and with statistical precision. The grand challenge for the scientific community is to understand the entire structural and functional design of the cell and fine-tune it for scientific applications ranging from basic to pharmaceutical. In a traditional experimental set-up, it is difficult to focus on more than one problem though recent high-throughput techniques have enabled investigation at the “whole” organism level. Nevertheless, data coming from these experiments are often noisy and require a large number of replicates to validate a single observation. Furthermore, the statistical treatment of the high-throughput data is also controversial. To overcome the physical and conceptual limitations, we need innovative sets of tools and strategies to address a problem. Recently, a spurt of articles published in Nature (Nov 14, 2002 issue) lends credibility to the idea of using in silico approaches for understanding and engineering whole cellular systems. E-Cell is one such tool that has been specifically designed to model and simulate cellular pathways. It has been successfully used to create a self-sustaining cell with 127 genes, that is, just stable enough for survival. In this chapter, some of the basic modeling concepts, their importance, the role of E-Cell, and the future challenges that await the modeling community will be discussed.


  • E-Cell;
  • Self-supporting Cell;
  • In Silico Modeling;
  • Mycoplasma Genitalium;
  • Virtual Erythrocyte;
  • Modeling;
  • Simulation