papers

ICSB06 poster: Numerical Simulation and Molecular Systems Biology

Poster at ICSB06.

ieeetak.pdf

# Computational challenges in cell simulation, Takahashi, K., Yugi, K., Hashimoto, K., Yamada, Y., Pickett, C., and Tomita, M., IEEE Intelligent Systems 17:5, 64-71, 2002. (Design rationale)

sugimoto2005.pdf

# Distributed Cell Biology Simulations with E-Cell System, Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, and Masaru Tomita, LSGRID04, Kanazawa, 2004. Also in Lecture Notes in Computer Science, Springer, 2005. (Running E-Cell on grid and cluster environments.)

takahashi-thesis.pdf

# Multi-algorithm, multi-timescals cell biology simulations, Takahashi, K., PhD Thesis, Keio University, 2004. (Design rationale, multi-algorithm simulation meta-algorithm, and E-Cell 3 implementation)

takahashi03-1.pdf

# A Multi-algorithm, Multi-timescale Method for Cell Simulation, Kouichi Takahashi, Kazunari Kaizu, Bin Hu, and Masaru Tomita, Bioinformatics, 20: 538-546, 2004. (A paper on Takahashi's multi-algorithm simulation method implemented in E-Cell 3.)

takahashi2005.pdf

# Space in systems biology of signaling pathways -- towards intracellular molecular crowding in silico, Takahashi, K., Arjunan, S.N.V., and Tomita, M., FEBS Letters, 579(8), 1783-1788, (2005). (Towards spatial modeling of intracellular biochemistry)

takahashi-cbsb07