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E-Cell 3.1.105

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Publisher Old version


August 9 2010


E-Cell 3.1.105


E-Cell is a concept of constructing virtual cells on computers.

E-Cell System is an object-oriented software suite for modeling, simulation, and Analysis of large scale complex systems such as biological cells, architected by Koichi Takahashi and written by a wonderful team of developers. Core part of the system, E-Cell Simulation Environment version 3, allows many components driven by multiple algorithms with different timescales to coexist.

E-Cell System consists of the following three major parts:

* E-Cell Simulation Environment (or E-Cell SE)
* E-Cell Modeling Environment (or E-Cell ME)
* E-Cell Analysis Toolkit

Complex nature of biological systems arises from Diversity of components and underlying rules, rather than emerging complexity from homogeneity and a few principles in physics and chemistry, characterize biology.

Software development for non-trivial cell simulation projects is a notably expensive process. For research projects in the traditional computational sciences, where brute force computation remains operative, it is reasonable to develop new software for each project, sometimes in a disposable fashion. Most of the traditional computational science fields like computational physics are characterized by numerous uniform components and a limited number of simple principles. Cell simulation, in contrast, involves numerous and various components with different properties, interacting in diverse, complicated manners. The design and implementation of simulation software inevitably reflects the complexity of the problem.

Software engineering can support the cellular simulation projects in many ways including: sophisticated modeling theory, well-designed software platform, data management methods, project management etc. E-CELL SE is our challenge to provide cell simulation / bioinformatics community with a SMART software platform.

The E-Cell development team in Institute for Advanced Bioscience, Keio University has received IBM Shared University Research Award 2003.

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