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The Wide-field Infrared Transient Explorer (WINTER) is a 1x1 degree infrared survey telescope under devel- opment at MIT and Caltech, and slated for commissioning at Palomar Observatory in 2021. WINTER is a seeing-limited infrared time-domain survey and has two main science goals: (1) the discovery of IR kilonovae and r-process materials from binary neutron star mergers and (2) the study of general IR transients, including supernovae, tidal disruption events, and transiting exoplanets around low mass stars. We plan to meet these science goals with technologies that are relatively new to astrophysical research: hybridized InGaAs sensors as an alternative to traditional, but expensive, HgCdTe arrays and an IR-optimized 1-meter COTS telescope. To mitigate risk, optimize development efforts, and ensure that WINTER meets its science objectives, we use model-based systems engineering (MBSE) techniques commonly featured in aerospace engineering projects. Even as ground-based instrumentation projects grow in complexity, they do not often have the budget for a full-time systems engineer. We present one example of systems engineering for the ground-based WINTER project, featuring software tools that allow students or staff to learn the fundamentals of MBSE and capture the results in a formalized software interface. We focus on the top-level science requirements with a detailed example of how the goal of detecting kilonovae flows down to WINTER's optical design. In particular, we discuss new methods for tolerance simulations, eliminating stray light, and maximizing image quality of a fly's-eye design that slices the telescope's focus onto 6 non-buttable, IR detectors. We also include a discussion of safety constraints for a robotic telescope.