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In the 21st century, computational thinking (CT) is of utmost importance, and pair programming has emerged as a popular method for teaching CT skills. This study aimed to understand the challenges faced by middle school students in acquiring essential CT elements through pair programming. To gather student insights, an open-ended survey was conducted with eighty-four eighth-grade students in the US. Results revealed numerous challenges in cognitive, affective, and social dimensions during the pair programming process, highlighting the need for increased support at the classroom, school, and district levels to ensure successful implementation of pair programming in middle schools. The study provides theoretical, practical, and methodological implications for CT education and pair programming, acknowledges limitations, and discusses opportunities for future research.