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In response to the need for a scalable, institutionally supported model of educational change, the Science Education Initiative (SEI) was created as an experiment in transforming course materials and faculty practices at two institutions--University of Colorado Boulder (CU) and University of British Columbia. We find that this departmentally focused model of change, which includes an explicit focus on course transformation as supported by a discipline-based postdoctoral education specialist, was generally effective in impacting courses and faculty across the institution. In CU's Department of Physics, the SEI effort focused primarily on upper-division courses, creating high-quality course materials, approaches, and assessments, and demonstrating an impact on student learning. We argue that the SEI implementation in the CU Physics Department, as compared to that in other departments, achieved more extensive impacts on specific course materials, and high-quality assessments, due to guidance by the physics education research group--but with more limited impact on the departmental faculty as a whole. We review the process and progress of the SEI Physics at CU and reflect on lessons learned in the CU Physics Department in particular. These results are useful in considering both institutional and faculty-led models of change and course transformation. [This paper is part of the Focused Collection on Upper Division Physics Courses.]