This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Cellular structure and function is determined by an array of interdependent biochemical reactions and processes, spatially distributed in a non-homogenous fashion within the cell. The Virtual Cell is a computational environment that allows a general approach for modeling the spatially organized and interdependent chemical processes that determine cell function. This new technology is designed to be accessible to the experimental cell biologist to create models that can serve as input to a numerical simulation of intracellular dynamics. Behind the scenes, there are complex transformations required to construct the corresponding mathematical model from the biological model and an experimental application . These consist of graph theoretic approaches, symbolic manipulation of equations and other algorithms that can optimally take advantage of the structure of the problem. New versions of these algorithms are regression tested against the thousands of models stored in the database. The numerical solution of these mathematical models are also under continuous development, and are tested using regression testing against a large set of models with known solutions. As we proceed in development of the Virtual Cell, we incorporate new modeling abstractions, new mathematical formalisms, new numerical techniques and new model analysis techniques.
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