A well-constructed, step-by-step protocol is a critical starting point for teaching undergraduates new techniques, an important record of a lab's standard procedures, and a useful mechanism for sharing techniques between labs. Many research labs use websites to archive and share their protocols for these purposes. Here we describe our experiences developing and using a protocol website for the additional purpose of enhancing undergraduate research training. We created our lab's protocol website in a message board format that allows undergraduates to post comments on protocols describing the lessons they learned, questions that arose, and/or insights they gained while learning to execute specific research protocols. Encouraging and expecting students to comment on the protocols they are learning to execute is beneficial for both the student and for the lab in which they are training. For the student, annotations encourage active reflection on their execution of techniques and emphasize the important message that attending to and understanding details of a protocol is a critical factor in producing reliable data. For the lab, annotations capture valuable insights for future generations of researchers by describing missing details, hints, and common hurdles for newcomers. (Contains 4 figures.)