This paper describes a design-based research project that investigates the learning of scientific knowledge about climate change through computational models. The design experiment used two NetLogo models and problem-based learning materials developed in partnership with a high school science teacher. In the study, three classes of year nine science students were divided into two groups based upon different levels of structure that was provided during learning activities with the models. The results indicate that there was significant learning of concepts about greenhouse gases and the carbon cycle through engagement with the models. We also describe the process analysis techniques being developed to analyze the log files of the interactions the students had with the computer models