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Martin Falk, Thomas Ertl (VISUS - Visualization Research Center, University of Stuttgart, Germany)
Cellular transport processes play an important role in systems biology. Effects of molecular crowding, hindered diffusion, and transport with motor proteins along filaments of the cytoskeleton are subjects to research. To setup a new model experimental data, theoretical considerations, and additional hypotheses are used. After simulating the model, an analysis employing different visualization techniques follows. Then, the model is validated by the user. Subsequently, the whole process is repeated beginning with model refinement and parameter adjustment. Our tool "CellVis" unifies the modeling stage and the visualization of cellular transport processes in one application easing the overall process. Modeling is supported by means of interactive graph editing. Visualization techniques, like tables, 3D visualizations, plots, etc., are used to validate simulation results and to gain new insights. The simulation, currently an external tool, will also be embedded in the near future allowing a direct coupling of modeling, simulation, and analysis. "CellVis" provides an userfriendly frontend to develop new models for particle simulations, especially for cellular transport processes.