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This study evaluates parameter estimation methodology in the context of neuronal signaling networks. Based on the results of a previous study, four parameter estimation methods, Evolutionary Programming, Genetic Algorithm, Multistart, and Levenberg-Marquardt, are selected. All the reaction rate constants of the test case, the protein kinase C (PKC) pathway model, are estimated using the selected four...
Several stochastic simulation tools have been developed recently for cell signaling. A comparative evaluation of the stochastic simulation tools is needed to highlight the current state of the development. In our study, we have chosen to evaluate three stochastic simulation tools: Dizzy, Systems Biology Toolbox, and Copasi, using our own MATLABreg implementation as a benchmark. The Gillespie stochastic...
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