Computer simulations in 3D image-derived geometries provide a complementary tool for studying biological processes in space and time, as outlined by Ivo F. Sbalzarini on pages 482–490 of this issue. The cover art shows a computer visualization of the 3D structure of the endoplasmic reticulum of a VERO cell. The 3D shape of this organelle has been reconstructed from confocal microscopy images using computational image-processing methods. Computer simulations then allow the study of dynamic processes in such realistic biological shapes, such as the diffusion of fl uorescent marker proteins in a fl uorescence recovery experiment. This enables one to perturb parameters of the system that are experimentally not controllable (such as the shape of the organelle) and observe quantities that are experimentally not observable. Ivo F. Sbalzarini provides an introduction to the, to many unfamiliar, world of computational biology, explaining commonly used terms and highlighting prospects and pitfalls.