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The Tenth q-bio Summer School - Albuquerque: Computer Lab 4
Introduction to modeling reaction-diffusion systems with MCell and CellBlender
James R. Faeder, University of Pittsburgh School of Medicine
In this tutorial participants will learn how to construct reaction-diffusion models of cell systems using CellBlender, which is a powerful graphical interface to the popular MCell simulator. MCell performs particle-based stochastic simulations of biochemical reactions with arbitrarily complex boundaries. Participants will learn how to construct simple geometries and reaction networks and also how to import more complex geometries derived from images and more complex reaction networks developed in BioNetGen. The tutorial will also introduce participants to a number of relatively simple models where spatial effects produce large deviations from the well-mixed limit and even emergent phenomena that are otherwise not observed.
