Readings

Overall / Underlying Design Philosophy

• Numerical Simulation and Molecular Systems Biology, Takahashi, K., International Conference on Systems Biology, Yokohama, Japan (2006). (What's simulation, what's reaction rates, why we can't get reaction rates well, and what we can do for this bottleneck.)
• 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)
• 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. Overrides IEEE 2002 and Bioinformatics 2004 papers below)
• 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)

E-Cell 3 Publications

• A paper on software implementation is under preparation...
• 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.)
• 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.)

E-Cell 1 and 2 Publications

• E-CELL: Software environment for whole cell simulation, Tomita,M., Hashimoto,K., Takahashi,K., Shimizu,T., Matsuzaki,Y., Miyoshi,F., Saito,K., Tanida,S., Yugi,K., Venter,J.C., Hutchison,C., Bioinformatics, 15:1, 72-84, 1999.
• "E-Cell 2: Multi-platform E-Cell Simulation System", K. Takahashi, N. Ishikawa, Y. Sadamoto, S. Ohta, A. Shiozawa, F. Miyoshi, Y. Naito, Y. Nakayama, M. Tomita, Bioinformatics, 19:13, 1727-1729, 2003.

Other E-Cell Project publications

This page has a complete listing of publications by E-Cell Project members.

Other E-Cell Project Readings

• To build a better model; Nature Methods 4:367-374 (2007)`
• Building Working Cells 'in Silico'; Science 284-5411 (2 Apr 1999) pp.80 - 81.
• Going for Grand Challenges; Nature 402 (2 Dec 1999) pp.C70.
• Computerized role models: Japan's push to create a virtual cell signals a new approach to research; Nature 417 (27 June 2002).

See here for more.