Simulation in systems biology

Kouichi Takahashi


Kouichi Takahashi, Ph.D., is a system architect of the E-Cell Simulation System at the Institute for Advanced Biosciences, Keio University, Japan. He has been leading the computational and algorithmic developments of the E-Cell Project, a scientific project developing necessary theoretical supports, technologies and software platforms to allow precise whole cell-scale simulation. He founded the project in 1996, and the E-Cell Consortium in 2002, with Prof. Masaru Tomita and colleagues. He is an initial member of the SBML (Systems Biology Markup Language) Forum. He earned his Ph.D. from Keio University in 2004.


Due to the complex nature of subsystems and the intimate couplings between them, biological systems pose some significant computational challenges, including the need for multi-scale and multi-formalism simulation techniques. E-Cell Simulation Environment Version 3 is a generic software platform for modeling, simulation and dynamical analysis in computational cell biology. The software implements a modular simulation 'meta-algorithm' based on Hermite integration, a discrete event scheduler, and object orientation, that can efficiently drive a simulation model consisting of many sub-models with different simulation algorithms and different timescales. Some applications of this simulation method, such as composite Gillespie/ODE simulations of an E.Coli heat-shock response model will be shown. Many useful numerical experiments in computational cell biology, such as metabolic control analysis (MCA), bifurcation analysis and kinetic parameter estimation, impose heavy computational loads. To cope with the huge amount of computation, the software platform can parallelize the simulation sessions transparently on shared-memory, Grid and cluster environments.


K. Takahashi et al, "Computational challenges in cell simulation", IEEE Intell. Syst., 17(5):64-71, 2002. PDF.
K. Takahashi et al, "A multi-algorithm, multi-timescale method for cell simulation", Bioinformatics, 20(4): 538-546, 2004. PubMed. PDF.