Graduate Engineering students need to understand and use the concepts and methods of applied research when they enter the engineering workforce. Using the principles of the Practical Inquiry Model (PIM) for such instruction can be effective in guiding such students in the research process to enhance their interest in and use of applied research methods. The PIM is a socio-constructivist approach that can enhance reflective thinking and collaboration to prepare them for their future workplace. To understand learning within the PIM, we examined students’ perceived cognitive presence during applied research activities. Cognitive presence consists of four levels including: triggering events, exploration, integration, and resolution. The majority PIM studies examined students' perceived cognitive presence in discussions in Education, Foreign Languages, or Professional Development. The field is still limited in research on how engineering students perceive cognitive presence in online courses. We believe that findings can fill the gap by providing more evidence about engineering students. This study developed and implemented a suite of customizable online learning modules to guide students in applied research. The learning modules were divided into three steps: research question, literature research, and conducting research using a generic template with the following sections: annotated open source learning materials, a random knowledge test with a pool of case study questions, a discussion board for brainstorming which required students to post their draft ideas, to comment on other students’ posts and integrate the comments in their submission, a self-reflection assignment to summarize the lesson learned, and a written assignment to organize their findings, make connections, elaborate ideas, and construct an argument based on their research. The modules were implemented in five courses in the Master of Science in Applied Information Technology program and in the Master of Science in Data Analytics Engineering at the ...