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:

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

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Manufacturer Web Site E-Cell System

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G6G Abstract Number 20622

G6G Manufacturer Number 104172