Inflammation is a key physiological and pathological response to disease and injury. Endophenotypes, broadly defined as intermediate traits (ideally heritable and manifesting prior to disease onset), can help us understand disease mechanisms as well as identify molecular therapeutic targets and prognostic indicators. Importantly, they can shed light on the causes of immune-mediated inflammatory diseases. I will cover research we have conducted involving population functional genomics approaches to understand the role and genetic basis of classic and non-classic markers of inflammation such as vitamin D and neutrophil counts. I will also discuss the application of best practice principles in research software engineering and applied statistical learning deriving from this research.