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Graduate engineering students need to cultivate collaborative and metacognitive skills for effective research before entering the workforce. This study examined differences between perceived Community of Inquiry (CoI) presences–teaching, social and cognitive– and shared metacognition when students participated in the pre-developed research learning modules. This study examined the differences between domestic and international students and in-person and online students across different STEM courses where research learning modules were integrated. The findings revealed statistical differences in perceived shared metacognition and three CoI presences between domestic and international students. However, we didn’t find any statistical differences between in-person and online students. The findings will help others who are interested in collaborative learning and shared metacognition for graduate engineering students.