E-CELL: Software Environment for Whole Cell Simulation

Masaru Tomita[1] (mt@sfc.keio.ac.jp)
Kenta Hashimoto[1] (kem@sfc.keio.ac.jp)
Kouichi Takahashi[1] (t94249kt@sfc.keio.ac.jp)
Tom Shimizu[1] (tom@sfc.keio.ac.jp)
Yuri Matsuzaki[1] (t94402ym@sfc.keio.ac.jp)
Fumihiko Miyoshi[1] (t95894fm@sfc.keio.ac.jp)
Kanako Saito[1] (t95401ks@sfc.keio.ac.jp)
Sakura Tanida[1] (t94613st@sfc.keio.ac.jp)
Katsuyuki Yugi[1] (t95980ky@sfc.keio.ac.jp)
J. Craig Venter[2] (venter@tigr.com)
Clyde A. Hutchison[2] (clyde@tigr.com)

[1] Laboratory for Bioinformatics Keio University
5322 Endo, Fujisawa, 252, Japan
[2] The Institute for Genomic Research
9712 Medical Center Drive Rockville, MD 20850, USA


Abstract

We present E-CELL, a generic computer software environment for modeling a cell and conducting experiments in silico. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, in terms of a set of reaction rules. The system then executes those reactions iteratively, and the user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell.

Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580kb genome sequence was determined at TIGR in 1995.

We discuss future applications of the E-CELL system with special respect to genome engineering.

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Japanese Society for Bioinformatics