Collaborative computer-based learning allows a group of users to access, share, and contribute content. A computer-based system can be accessed by a community of users over a communications network. A data storage device can store data comprising items of teaching content and items of user content, such that the data is accessible by the community of users. A set of collaborative system tools can provide users with the ability to create an item of user content associated with items of teaching content or with other items of user content. An annotation mechanism can provide users with the ability to comment on items of teaching content or items of user content in the form of an annotation that is then stored in the data storage device. The annotation mechanism is configured to merge the annotation with the associated item of teacher or user content and generate merged content with the annotation overlaid on the associated item of teacher or user content.