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 wholecell

Abstract 
Central to the postgenomic 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 markup 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 largescale 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 highthroughput
quantitative experimental data and database of mathematical models
(ECell in silico model database), generating dynamical models ready
for simulation experiments using software systems such as ECell
Simulation Environment. In this talk, I will also introduce related
researches in the ECell Project.
References;
1. Arakawa K, et al., GEM System: Automatic prototyping of cellwide
metabolic pathway models from genomes, BMC Bioinformatics, 2006,
7:168
2. Arakawa K, Tomita M, Glanguage System as a platform for largescale
analysis of highthroughput omics data, Journal of Pesticide Science,
2006, 31(3):282288
3. Ishii N, et al., Multiple HighThroughput Analyses Monitor the
Response of E. coli to Perturbations, Science, 2007, 316(5824):
593597

