Multiscale modeling is required for linking physiological processes operating at the organ and tissue levels to signal transduction networks and other subcellular processes. Several XML markup languages, including CellML, have been developed to encode models and to facilitate the building of model repositories and general purpose software tools. Progress in this area is described and illustrated with reference to the heart Physiome Project which aims to understand cardiac arrhythmias in terms of structure-function relations from proteins up to cells, tissues and organs.