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.