E-CELL project: Towards integrative simulation of cellular processes

Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, S. Shimizu, Yoichi Nakayama

Research output: Contribution to conferencePaper

Abstract

A general framework for modeling gene expression using the E-CELL system is presented. Using the framework, the following three gene regulation systems: the lac operon and the araBAD operon of E. coli, and the lytic-lysogenic switch network in bacteriophage λ, are modelled and simulated. E-CELL simulates the behavior of model cell by computing interactions among molecular species it contains and allows the user to define chemically discrete compartments such as membranes, chromosomes, and cytoplasm. A detailed model of the gene expression process as a part of the self-supporting cell model is constructed. To simulate complex gene regulation systems with a large number of genes, a more abstract and simpler model is desired for the sake of efficiency.

Original languageEnglish
Pages290-298
Number of pages9
Publication statusPublished - 2000 Jan 1
EventRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology - Tokyo, Jpn
Duration: 2000 Apr 82000 Apr 11

Other

OtherRECOMB 2000: 4th Annual International Conference on Computational Molecular Biology
CityTokyo, Jpn
Period00/4/800/4/11

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ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Tomita, M., Hashimoto, K., Takahashi, K., Matsuzaki, Y., Matsushima, R., Yugi, K., Miyoshi, F., Nakano, H., Saito, Y., Shimizu, S., & Nakayama, Y. (2000). E-CELL project: Towards integrative simulation of cellular processes. 290-298. Paper presented at RECOMB 2000: 4th Annual International Conference on Computational Molecular Biology, Tokyo, Jpn, .