## E-Cell System

** Category** Cross-Omics>Agent-Based Modeling/Simulation/Tools

** Abstract** The E-Cell System is an object-oriented (OO) software suite for modeling, simulation, and analysis of large scale complex systems such as biological cells.

The E-Cell System allows many components that are driven by multiple algorithms with different timescales to coexist in a model.

Unlike its preceding versions, E-Cell Version 1 and Version 2, Version 3 (the current version) can:

1) Run cell models consisting of sub-models driven asynchronously by different simulation algorithms;

2) Provide Python scripting Application Programming Interfaces (APIs) for various purposes (such as front-end, simulation procedure, and distributed computation APIs); and

3) Allow for two (2) different levels of parallel computations, namely:

- a) A shared-memory discrete-event parallelism of a single simulation run; and
- b) Parallelization of computationally intensive simulation experiments, such as parameter tuning, metabolic control and bifurcation analyses, on various middleware including the Sun Grid Engine (SGE).

Support for the Globus toolkit is under development -

The Globus® Toolkit is an open source software toolkit used for building grids. It is being developed by the Globus Alliance and many others all over the world.

A growing number of projects and companies are using the Globus Toolkit to unlock the potential of grids for their cause.

Architecture of the E-Cell System --

The E-Cell System consists of the following three (3) major components:

1) E-Cell Simulation Environment (E-Cell SE), which runs the simulation and provides scripting APIs;

2) E-Cell Modeling Environment (E-Cell ME), that helps users to conduct a collaborative modeling of large-scale cell models; and

3) E-Cell Analysis Toolkit, a library of mathematical analysis scripts for E-Cell SE.

Note: The E-Cell System’s main development platform is Linux.

However, a Windows NT/XP version is available, and porting projects are ongoing for other operating systems including Mac OS X and IBM AIX.

E-Cell System - Multi-Algorithm Simulation Method --

The fundamental simulation algorithm used in E-Cell System Version 3 is a modular, object-oriented simulation meta-algorithm based on a discrete-event scheduler and Hermite polynomial interpolation.

See the following paper for additional information:

[Takahashi, K, Kaizu, K, Hu, B, and Tomita, M (2004). A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics, 20(4):538-46]

With this ‘meta-algorithm’, the E-Cell System can efficiently handle a model that consists of many sub-models with different algorithms and different time-scales.

Virtually any time-driven simulation algorithm can be implemented as a plug-in of E-Cell SE, and used in any combination.

The current version of the software is shipped/down-loaded with the following simulation algorithms:

1) Several variations of Ordinary Differential Equation (ODE) and Differential Algebraic Equation (DAE) solvers;

2) Gillespie-Gibson stochastic simulation algorithm;

3) ESSYNS GMA/S-System power-law canonical differential equation solver;

4) A discrete-time simulator; and

5) A hybrid dynamic/static pathway simulation method.

*System Requirements*

Contact manufacturer.

*Manufacturer*

- Institute for Advanced Bioscience (IAB)
- Keio University
- Tsuruoka 997-0035, Japan

** Manufacturer Web Site**
E-Cell System

** Price** Contact manufacturer.

** G6G Abstract Number** 20622

** G6G Manufacturer Number** 104172