A GENERAL COMPUTATIONAL FRAMEWORK FOR MODELING CELLULAR STRUCTURE ANDFUNCTION

The ''Virtual Cell'' provides a general system for testing cell biolog ical mechanisms and creates a framework for encapsulating the burgeoni ng knowledge base comprising the distribution and dynamics of intracel lular biochemical processes. It approaches the problem by associating biochemical and electrophysiological data describing individual reacti ons with experimental microscopic image data describing their subcellu lar localizations. Individual processes are collected within a physica l and computational infrastructure that accommodates any molecular mec hanism expressible as rate equations or membrane fluxes. An illustrati on of the method is provided by a dynamic simulation of IP3-mediated C a2+ release from endoplasmic reticulum in a neuronal cell. The results can be directly compared to experimental observations and provide ins ight into the role of experimentally inaccessible components of the ov erall mechanism.