Virtual Cell: computational tools for modeling in cell biology

Abstract The Virtual Cell (VCell) is a general computational framework for modeling physicochemical and electrophysiological processes in living cells. Developed by the National Resource for Cell Analysis and Modeling at the University of Connecticut Health Center, it provides automated tools for simulating a wide range of cellular phenomena in space and time, both deterministically and stochastically. These computational tools allow one to couple electrophysiology and reaction kinetics with transport mechanisms, such as diffusion and directed transport, and map them onto spatial domains of various shapes, including irregular three‐dimensional geometries derived from experimental images. In this article, we review new robust computational tools recently deployed in VCell for treating spatially resolved models. WIREs Syst Biol Med 2012, 4:129–140. doi: 10.1002/wsbm.165 This article is categorized under: Models of Systems Properties and Processes > Cellular Models Analytical and Computational Methods > Computational Methods Models of Systems Properties and Processes > Mechanistic Models