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The Defense Advanced Research Projects Agency (DARPA) High Productivity Computing Systems (HPCS) Program sponsored a series of case studies to identify the life cycles, workflows, and technical challenges of computational science and engineering code development representative of the program’s participant and to identify “lessons learned” that can be transferred to the general computational science and engineering community to improve development of such codes. The NENE code is a physics-based application code for analyzing and predicting the complex behavior and interaction of individual physical systems and individual particles in the systems for the purpose of design and analysis of such systems. The core NENE development team is of moderate size, is expert, and is agile. NENE is an example of a distributed development project; the core team is anchored at a university, but as many as 250 individual researchers have made contributions from other locations.