In his editorial overview for the 2008 Special Issue on this topic, the late Jaroslav Stark pointedly noted that systems biology is no longer a niche pursuit, but a recognized discipline in its own right “noisily” coming of age [1]. Whilst general underlying principles and basic techniques are now reasonably well established, we see a progressive shift from “fishing expeditions” through seas of “omics” data towards increasingly more model-driven research generating verifiable hypotheses that are iteratively tested and refined across different aggregation levels. In this special issue, we illustrate this ethos of systems biology at work in various fields through an eclectic series of articles thematically grouped under “methods and tools in network analysis”, “emerging and enabling technologies”, “microbes in disease and the environment”, “human health and disease” and “synthetic biology”.