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Systems Biology Laboratory

Date of Establishment: July 1, 2002
Director: Masaru Tomita
Contact: Keio University Shonan-Fujisawa Campus


In recent years, bioinformatics, in particular cell modeling computer simulation, has been attracting attention as a new methodology to understand the dynamic behavior of complex intra-cell metabolism. This will be one of the most important technologies in the 21st century in terms of its applications to various industries including medical care, the development of drugs, industrial applications of microorganisms and environmental purification. SFC started the "E-CELL project" for cell simulation in 1995, developed the base software for simulation and constructed various cell metabolic models using this software. However, software technology and modeling technology for cell simulation are still under development and there are a lot of problems that need to be solved before a large-scale cell model can be constructed. The Research Institute aims to lead the world in this field by gathering software technologies and biotechnologies in Japan.

Research Plan

First year

A fully-fledged cell metabolism model will be developed by conducting comprehensive metabolome analysis on cell metabolism through gathering knowledge and methodologies about cell simulation, metabolism engineering, analysis engineering and genome engineering. The developed model is expected to be a potent tool for CAD (computer aided design) of useful microorganisms, the identification of microorganisms suitable for industrial applications, construction of precise simulation models, and the incubation of microorganisms in a controlled manner to obtain highly reproducible data. Only a small amount of data has been available for creating precise models intra-cell metabolic material consisting mainly of smaller molecules. To comprehensively measure the density of metabolic intermediate materials, the Metabolism Engineering Group conducts controlled incubation with high reproducibility using a bioreactor to obtain samples. The analysis chemical group measures these specimens using base technologies so far developed for comprehensive measurement. The Bioinformatics Group is constructing a model based on data obtained from comprehensive measurements, developing a new version of a cell simulation environment: E-CELL, and the group is planning to release the 3rd beta version soon. Construction of simulations and models will proceed while improving the environment and database development for building a large-scale model.

Second year

On receiving simulation results and predictions, the Gene Engineering Group involved in the development of technologies to reform microorganisms will promote improvement of a deletion strain series of E.Coli. and establish large-scale reform technology of the Bacillus subtilis genome.

Third year

New statistics shall be constructed based on considerations of results of the first and second years.


Name Affiliation
o Masaru Tomita Professor, Faculty of Environment and Information Studies
Mitsuyasu Itaya Professor, Faculty of Environment and Information Studies
Akio Kanai Professor, Faculty of Environment and Information Studies
Tomoyoshi Soga Professor, Faculty of Environment and Information Studies
Yasuhiro Naito Associate Professor, Faculty of Environment and Information Studies