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E-Cell: Computer Simulation of the Cell

Systems Biology

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

Published Online: 15 MAR 2012

DOI: 10.1002/3527600906.mcb.200300061.pub2

Reviews in Cell Biology and Molecular Medicine

Reviews in Cell Biology and Molecular Medicine

How to Cite

Dhar, P. K., Takahashi, K., Nakayama, Y. and Tomita, M. 2012. E-Cell: Computer Simulation of the Cell. Reviews in Cell Biology and Molecular Medicine. .

Author Information

  1. 1

    School of Biomedical Sciences, Symbiosis International University, Pune,, India

  2. 2

    Keio University, Institute for Advanced Biosciences, Tsuruoka, Yamagata, Japan

Publication History

  1. Published Online: 15 MAR 2012


Cells are massively parallel and massively interactive systems. The grand challenge is to understand their structural and functional design and to use the knowledge acquired to build useful applications. In traditional settings, it was difficult to focus on more than one gene at a time, but recently developed high-throughput technologies have enabled studies to be conducted at the whole organism level. Nevertheless, data from these experiments are often noisy and require a large number of replicates to validate even a single observation. Furthermore, the statistical treatment of high-throughput data is also error-prone. To overcome the physical and conceptual limitations, there is a need to develop strategies and tools to address complex biological problems. Systems Biology studies conducted during the past decade have lent credibility to an in-silico approach for understanding and engineering whole-cell systems. The E-Cell platform has been specifically designed to address network-based problems. The E Cell has been used successfully 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 of the modeling community, will be discussed.


  • E-cell;
  • Self-supporting cell;
  • In-silico modeling;
  • Mycoplasma genitalium ;
  • Virtual erythrocyte;
  • Modeling;
  • Simulation