Shoot apical meristems (SAMs) are populations of dividing, undifferentiated cells that generate organs at the tips of stems and branches throughout the life of the plant. As they define the number, type and position of lateral organs, meristems are the basis of plant architecture, allowing plants to adapt their development to their environment. In particular during the last decade, an impressive body of knowledge concerning shoot apical meristem function has been generated. This concerns information on the genes involved, their expression patterns, cell differentiation, cell division patterns, etc. The complexity of these data is such that an integrated view of meristem function is not yet possible. Therefore, adapted mathematical and informatics approaches are now required to integrate the knowledge in such a way that it can advance the level of understanding in the field. To formulate and test hypotheses on spatial and temporal aspects such as flows of signalling molecules between cells, strain within tissues, and the role of gene products in the spatial control of cell proliferation, we are creating a virtual meristem that will integrate as much spatial, dynamic and quantitative information as possible.