document: 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
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