Precise, robust and entrained circadian timing of bodily functions down to the cellular and molecular scale is pivotal for ensuring efficient use of resources by an organism in pursuit of optimal evolutionary fitness. In mammals, such circadian timing is governed by the suprachiasmatic nuclei (SCN) containing approximately 20,000 cells which are heterogeneous in their expression of signalling molecules, rhythmic properties and connectivity to one another. It is through emergent network properties that the diversity of cells is able to synchronise cell-autonomous rhythms and generate an ensemble signal that is conveyed to local clocks in peripheral tissues and brain areas. Whilst previous research has focused on pinpointing the potential role of individual elements of the SCN circuitry, this PhD sought to utilise cutting-edge advances in research tools to view the network in its entirety. Transcriptional analysis of the SCN at single cell resolution was performed to address a) which molecular elements define functional network components in the SCN, b) which signalling molecules and pathways are used to connect SCN network components and c) whether there is a circadian shift in neurochemical topology. Furthermore, to visualise direct connectivity within defined neurochemical cells of the SCN the pseudotyped rabies virus tracing tool was successfully used in the SCN for the first time. In tracing pre-synaptic connectomes of SCN cells their spatial arrangement, extent and composition were characterised. In so doing, I was able to define cell-type molecular properties in the mammalian SCN at two opposing circadian time-points. Eight distinct SCN sub-populations were identified and signalling axes between these inferred. Small-world network topology was confirmed and novel network modulating effects of components were identified. Specifically, Prokineticin 2 cells were shown to display pace-making potential within the SCN; they were not only able to modulate an ongoing network rhythm but can also initiate network rhythmicity in an otherwise arrhythmic SCN. In establishing a dataset holding information on the transcriptional profiles of individual SCN cells, and developing a synaptic tracing tool within the SCN, I have been able to define elements, trace connectivity and identify novel functional roles of circuit components to increase our understanding of the topology of the mammalian master oscillator.