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Position TitleBiological simulation using parallel computing with Matlab and R
SummaryThe intern will develop codes for model simulation, visualization and testing in both Matlab and R, including the Matlab Parallel Computing Toolbox and various packages supporting parallel computing in R. Additional tools for constructing and managing models in a model markup language (SBML, MathML, CellML) will be utilized in order to make the resulting models portable.
Job DescriptionA previously published model of C3 carbon metabolism in plants will be reconstructed in Matlab and R. In the original publication this model was simulated deterministically and the the allocation of proteins was optimized for maximum carbon fixation. This internship project will involve helping to extend the original study by implementing a stochastic simulation of this biochemical system.
The intern will help to implement and evaluate the behavior of the stochastic simulation and compare it to the deterministic version. The intern will also help to implement an optimization approach that will seek to optimize protein allocation for the stochastic version of the model.
The Matlab Parallel Computing Toolbox and various packages supporting parallel computing in R will be used to evaluate the performance gains of parallelizing simulation and optimization procedures.
Start Date05/23/2010
End Date05/15/2011
LocationNorth Carolina Agricultural and Technical University in Greensboro, NC and Shodor in Durham, NC.
Interns