A general computational framework for modeling cellular structure and function

Abstract

The "Virtual Cell" provides a general system for testing cell biological mechanisms and creates a framework for encapsulating the burgeoning knowledge base comprising the distribution and dynamics of intracellular biochemical processes. It approaches the problem by associating biochemical and electrophysiological data describing individual reactions with experimental microscopic image data describing their subcellular localizations. Individual processes are collected within a physical and computational infrastructure that accommodates any molecular mechanism expressible as rate equations or membrane fluxes. An illustration of the method is provided by a dynamic simulation of IP3-mediated Ca2+ release from endoplasmic reticulum in a neuronal cell. The results can be directly compared to experimental observations and provide insight into the role of experimentally inaccessible components of the overall mechanism.

Mechanisms underlying the toxic effects of antimony species in human embryonic kidney cells (HEK-293) and their comparison with arsenic species

“…The data FRAP analysis was processed using the VirtualFRAP toolbox of Virtual Cell, which was developed by the University of Connecticut Health Center (Schaff et al, 1997(Schaff et al, , 2009). …”

Space as the final frontier in stochastic simulations of biological systems

“…We attempt in this review to present the stateof-the-art of such general-purpose software, describing the modeling methodology, highlighting the approximations inherent to modeling objects of such complex nature, and presenting perspectives of refinement. References are made to the following actively developed and freely available programs: Virtual Cell [7], E-Cell [8], MCell [9], Smoldyn [10], MesoRD [11], and STOCHSIM [12] as well as SmartCell [13], developed in our lab as a tool to analyze stochastic spatially relevant biological processes (see Table 1). …”

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)

“…microscale), the spatial partial differential equations (spatial PDEs) approach computes the intracellular kinetics at the macroscopic level. The Virtual Cell (Schaff et al, 1997(Schaff et al, , 2001Slepchenko et al, 2003) employs PDEs with the finite volume method (Smith, 1986) to perform reaction and diffusion of mobile molecules in its spatial simulation framework. Compartments in the framework can depict the spatial structures of the system.…”