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- W2080756773 abstract "The aim of this work is to create data- and experiment-driven simulation software that leverages kinetic models of intracellular processes. There is a need for specific tools that combine descriptions of mechanistic hypotheses of cellular physiology with detailed descriptions of experimental protocols and manipulations. We used components and technologies from the Virtual Cell platform (VCell; http:/vcell.org/), which was designed to provide a separation of layers representing biological models, physical mechanisms, geometry, mathematical models and numerical methods. We are developing standalone software packages for kinetic model-assisted simulation, analysis, and interpretation of common experimental protocols. The initial focus is on fluorescence microscopy - the Virtual Microscopy suite. The first prototype is the “Virtual FRAP” tool. This is a mostly data-centric experiment analysis framework that allows incorporating fluorescence microscopy (instrumentation, indicators, labels) into existing models of cellular physiology. The microscopy data is formally represented, and it is used to derive cellular geometry, distributions of molecules, and to perform quantitative comparisons with simulated model predictions. This overcomes the limitations of “traditional” approaches that use simplified parameterized “models” with closed-form analytical solutions. Such a customized environment combines powerful experiment description and analysis features with the flexibility of simulating more general classes of spatial models." @default.
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- W2080756773 date "2009-02-01" @default.
- W2080756773 modified "2023-10-11" @default.
- W2080756773 title "Virtual FRAP - an Experiment-Oriented Simulation Tool" @default.
- W2080756773 doi "https://doi.org/10.1016/j.bpj.2008.12.046" @default.
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