This set of reports were first presented as talks in two ‘Featured Topic’ symposia at the Experimental Biology (EB) meeting in April 2011 in Washington DC, USA. These two symposia grew out of an earlier US–Japan Brain Research Cooperative Program Workshop held at the Okinawa Institute of Science and Technology (OIST) in October 2010. The US National Institutes of Health (NIH) and the Japanese Science and Technology Agency (JST) jointly sponsored this OIST workshop to initiate and explore opportunities at the interface of neuroscience and systems biology, with the intention of follow-up meetings such as the present symposia. The OIST US–Japan workshop was organized by Dr Bruce Lindsey (University of South Florida, FL, USA) and the authors together with Erik DeSchutter (OIST, Onna, Japan). The OIST US–Japan workshop had two main themes, which then became the titles of the two aforementioned EB Featured Topics symposia: Multi-scale Modeling and Systems Biology of Synapses, chaired by James Schwaber, and Multi-scale Neuronal Control of Respiratory Function: Bridging Gene Networks to Neural Networks, chaired by Kendall Morris. At our previous OIST workshop, we concluded that we had ‘made a start’ on these issues, and during the EB Featured Topic sessions we continued discussing and presenting bridging opportunities in methods and approaches that are applicable in systems biology practice and neuroscience. Specifically, the symposia examined how modelling of molecular processes can provide a foundation for understanding adaptive electrical behaviour of neurons, and how unbiased global data can be useful in deciding which receptors, channels and transmitters need to be considered in a simplified schematic of a functional neuronal group. The apparent disconnect between computational neuroscience and systems biology has been observed previously and discussed at length in an article by Dr De Schutter, a featured presenter in the systems biology symposium (De Schutter, 2008). Commonly, computational neuroscience focuses on membrane models of different transmitter–receptor interactions and the effects of modulators (serotonin, etc.) on synaptic transmission and their impact on network behaviour, while systems biology focuses more deeply on signalling and genetic processes. Despite the conspicuous connections between neuronal membrane composition, signalling and gene expression, there is little bridging of this gap. The workshop was concerned with the commonalities between multiscale modelling of molecular processes and neuronal systems physiology. Our aim was to explore how robust function emerges from complex, plastic processes by combining computational neuroscience and the systems biology of functional, adaptive molecular processes. In order to consider these and related issues, the OIST US–Japan workshop, and now the two EB Featured Topic symposia, were organized around the following two ‘focal points’.