The E-CELL project: Towards integrative simulation of cellular processes

New Generation Computing - 2000
Masaru Tomita1,2, Kenta Hashimoto1,3, Koichi Takahashi3,1, Yuri Matsuzaki1,3, Ryo Matsushima1,3, Kanako Saito1,3, Katsuyuki Yugi1,3, Fumihiko Miyoshi1,3, Hisako Nakano1,4, Sakura Tanida1,2, Yusuke Saito1,2, Akiko Kawase1,2, Naoko Watanabe1,2, Thomas S. Simizu1,5, Yoichi Nakayama1,2
1Laboratory for Bioinformatics, Keio University, Fujisawa, Japan
2Department of Environmental Information, Keio University, Fujisawa, Japan
3School of Media and Governance, Keio University, Fujisawa, Japan
4Department of Policy Management, Keio University, Fujisawa, Japan
5Department of Zoology, Cambridge University UK

Tóm tắt

The E-CELL project was launched in 1996 at Keio University in order to model and simulate various cellular processes with the ultimate goal of simulating the cell as a whole. The first version of the E-CELL simulation system, which is a generic software package for cell modeling, was completed in 1997. The E-CELL system enables us to model not only metabolic pathways but also other higher-order cellular processes such as protein synthesis and membrane transport within the same framework. These various processes can then be integrated into a single simulation model. Using the E-CELL system, we have successfully constructed a virtual cell with 127 genes sufficient for “self-support”. The gene set was selected from the genome of Mycoplasma genitalium the organism having the smallest known genome. The set includes genes for transcription, translation, the glycolysis pathway for energy production, membrane transport, and the phospholipid biosynthesis pathway for membrane structure. The E-CELL system has been made available for beta testing from our website (http: //www.e-cell.org).

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