Computational challenges in cell simulation: a software engineering approach

Molecular biology´s advent in the 20th century has exponentially increased our knowledge about the inner workings of life. We have dozens of completed genomes and an array of high-throughput methods to characterize gene encodings and gene product operation. The question now is how we will assemble the various pieces. In other words, given sufficient information about a living cell´s molecular components, can we predict its behavior? We introduce the major classes of cellular processes relevant to modeling, discuss software engineering´s role in cell simulation, and identify cell simulation requirements. Our E-Cell project aims to develop the theories, techniques, and software platforms necessary for whole-cell-scale modeling, simulation, and analysis. Since the project´s launch in 1996, we have built a variety of cell models, and we are currently developing new models that vary with respect to species, target subsystem, and overall scale.