The dune-copasi solver is used to simulate models. This solves the PDE on a triangular mesh using finite element discretization methods. See the simulator documentation for more information on the available options when using it in the GUI. For more technical information about the DuneCopasi solver itself, see the dune-copasi website.
Starting from a segmented image of the compartments in the model, the boundaries are automatically identified and simplified, and from them a triangular mesh approximation to the geometry is constructed. For more details see the mesh documentation.