Two facets of systems biology are the generation of increasingly comprehensive network maps of the physical and functional interactions between biomolecules in cells, and the development of quantitative models of processes based on a detailed mechanistic understanding of a given pathway. However, only for few biological processes the mechanistic knowledge is sufficient to enable quantitative modeling. On the other hand incorporating proteome-scale network-based connections into quantitative models is difficult, in part due missing knowledge on the functional effects, physiological context, and biological consequences of mapped interactions. At this conference we will discuss novel computational and experimental approaches to bridge this ‘mechanistic gap’ and hear about current trends in network mapping and analysis.