Chapter category:

Foundations of E‑Cell Simulation Environment Architecture

This chapter appears in the following book:

E-Cell System: Basic Concepts
and Applications

Edited by: Satya Nanda Vel Arjunan, Pawan K. Dhar and Masaru Tomita
ISBN: TBA
» Get more information about this book at landesbioscience.com «

Chapter authors:
Nathan Addy and Koichi Takahashi

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The thorough overview of the E‑Cell Simulation Environment in this chapter provides a foundation for understanding the systems biology research that uses the E‑Cell Simulation Environment presented within this book. To begin this inquiry, we open with the most general question possible: what is the E‑Cell Simulation Environment? The answer is that the E‑Cell Simulation Environment (commonly abbreviated E‑Cell SE, or even SE) is a simulator of cellular systems models. It is the primary component of a three‑program software platform, collectively called the E‑Cell System, for creating, simulating and analyzing biological models. As the simulator in this larger environment, the E‑Cell Simulation Environment takes user‑defined abstract model descriptions, translates them into its own internal model format and calculates trajectories of those models through time, either by recording the results in a file for future analysis, or in real time where the model state can be viewed or modified by the user at any point during execution.

Nathan Addy
Molecular Sciences Institute

Koichi Takahashi
Molecular Sciences Institute

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Chapter category:

Foundations of E‑Cell Simulation Environment Architecture

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