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In iteration 2 of a design-based research, we investigated how regulative and cognitive scaffolds integrated within a wiki would help collaborative groups to co-construct scientifically sound and explanatory knowledge. This research was conducted in 5 secondary school classrooms and the curriculum topic was Climate Change. During an extended collaborative inquiry, students in 14 small groups used planning pages, reflections, and a wiki page template to plan for, conduct and monitor their inquiry and the quality of their progressive inquiry report. Overall, scientific quality of shared knowledge was improved comparing to iteration 1. In-depth analysis of knowledge co-construction processes in two groups showed that the designed scaffolds could have raised students awareness of the quality of their contributions to group work.