ゲノム情報科学研究教育機構  アブストラクト
Date September 10, 2007
Speaker Dr. Kazuharu Arakawa, Institute for Advanced Biosciences, Graduate School of Media and Governance, Keio University
Title Comprehensive modeling environment for the simulation of whole-cell
Abstract   Central to the post-genomic researches is the integrative understanding of living systems through systems biology approach, which requires mathematical formulation of the subject through a process called "modeling". Modeling in systems biology consists of four stages:
1. qualitative modeling of intracellular networks with omics data, 2. quantitative modeling through mathematical formulation of dynamical reactions, 3. cellular programming in model mark-up languages such as SBML in order to simulate the model, and 4. evaluations of the simulation results for the reconstruction of models. Currently most of these modeling practices are manually conducted, which becomes a major bottleneck in systems biology researches.
  For this purpose, we have developed an automated software system designated the GEM System for the modeling of metabolic pathways in bacteria, which reconstructs large-scale qualitative pathway models ready for metabolic flux analysis, by integrating omics data utilizing KEGG database as its basis. We are currently extending the modeling system to include quantitative information with high-throughput quantitative experimental data and database of mathematical models (E-Cell in silico model database), generating dynamical models ready for simulation experiments using software systems such as E-Cell Simulation Environment. In this talk, I will also introduce related researches in the E-Cell Project.

References;
1. Arakawa K, et al., GEM System: Automatic prototyping of cell-wide metabolic pathway models from genomes, BMC Bioinformatics, 2006, 7:168
2. Arakawa K, Tomita M, G-language System as a platform for large-scale analysis of high-throughput omics data, Journal of Pesticide Science, 2006, 31(3):282-288
3. Ishii N, et al., Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations, Science, 2007, 316(5824): 593-597
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