Based on recent education reform guidelines to prepare professionals who are able to handle new technological, economic, social, and environmental challenges, pedagogical modifications are deemed necessary by the educators. Specifically, in biology, the rapid changes in the content and biological products demand changes in the curriculum. We aim to address this current need by providing an example of a course that was redesigned to meet the current trends of biological engineering education. In this course-based undergraduate research experience (CURE), learning objectives and possible outcomes were developed and assessment mapping was performed to align the course objectives with the Accreditation Board for Engineering and Technology (ABET) recommendations. A description of how one can assess authentic inquiry courses while adhering to the recommendations are discussed. For example, in this particular course, students completed weekly reflection assignments, maintained lab notebooks that were graded every week, presented their research to their peers at the end of the semester, and submitted a final paper to be graded. "Holistic" engineering is crucial for the all-around development of a 21st century engineer. Altering the traditional lecturing with more hands-on learning is crucial for the development of professional and communication skills of students. Such alterations could lead to the production of well-rounded life-long learners to serve the upcoming world.