E-CELL project: Towards integrative simulation of cellular processes

Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Kanako Saito, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Sakura Tanida, Yusuke Saito, Akiko Kawase, Naoko Watanabe, Thomas S. Shimizu, Yoichi Nakayama

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

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 Mycoplasm 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).

Original languageEnglish
Pages (from-to)1-12
Number of pages12
JournalNew Generation Computing
Volume18
Issue number1
Publication statusPublished - 2000

Fingerprint

Pathway
Membrane
Genes
Gene
Cell
Genome
Glycolysis
Simulation
Phospholipids
Protein Synthesis
Biosynthesis
Simulation System
Software Package
Transcription
Simulation Model
Membranes
Membrane structures
Higher Order
Sufficient
Testing

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Hardware and Architecture
  • Theoretical Computer Science

Cite this

Tomita, M., Hashimoto, K., Takahashi, K., Matsuzaki, Y., Matsushima, R., Saito, K., ... Nakayama, Y. (2000). E-CELL project: Towards integrative simulation of cellular processes. New Generation Computing, 18(1), 1-12.

E-CELL project : Towards integrative simulation of cellular processes. / Tomita, Masaru; Hashimoto, Kenta; Takahashi, Koichi; Matsuzaki, Yuri; Matsushima, Ryo; Saito, Kanako; Yugi, Katsuyuki; Miyoshi, Fumihiko; Nakano, Hisako; Tanida, Sakura; Saito, Yusuke; Kawase, Akiko; Watanabe, Naoko; Shimizu, Thomas S.; Nakayama, Yoichi.

In: New Generation Computing, Vol. 18, No. 1, 2000, p. 1-12.

Research output: Contribution to journalArticle

Tomita, M, Hashimoto, K, Takahashi, K, Matsuzaki, Y, Matsushima, R, Saito, K, Yugi, K, Miyoshi, F, Nakano, H, Tanida, S, Saito, Y, Kawase, A, Watanabe, N, Shimizu, TS & Nakayama, Y 2000, 'E-CELL project: Towards integrative simulation of cellular processes', New Generation Computing, vol. 18, no. 1, pp. 1-12.
Tomita M, Hashimoto K, Takahashi K, Matsuzaki Y, Matsushima R, Saito K et al. E-CELL project: Towards integrative simulation of cellular processes. New Generation Computing. 2000;18(1):1-12.
Tomita, Masaru ; Hashimoto, Kenta ; Takahashi, Koichi ; Matsuzaki, Yuri ; Matsushima, Ryo ; Saito, Kanako ; Yugi, Katsuyuki ; Miyoshi, Fumihiko ; Nakano, Hisako ; Tanida, Sakura ; Saito, Yusuke ; Kawase, Akiko ; Watanabe, Naoko ; Shimizu, Thomas S. ; Nakayama, Yoichi. / E-CELL project : Towards integrative simulation of cellular processes. In: New Generation Computing. 2000 ; Vol. 18, No. 1. pp. 1-12.
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