Foundations of E-Cell Simulation Environment Architecture

Abstract

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.