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In recent years, research has focused on understanding how learners can benefit from tools that can assist in the development of informal reasoning skills when constructing arguments in collaborative learning with web-based learning environments. A common approach taken by each of these systems is to use support mechanisms (scaffolding) to facilitate student learning through the development of improved reasoning and argumentation skills. The authors of this paper have been developing computer-based learning environments for the past ten years, and have developed several award winning CD-ROM packages that feature a range of cognitive tools designed to assist learning. The development of these products has provided a rich source of information about learner use of cognitive tools. Our research has shown that two recurring issues keep emerging: 1. There is a need to develop generic cognitive tools that assist learners to understand and solve problems that relate to different knowledge domains. 2. There is a need to help learners to analyse and structure information gathered, when they use cognitive tools. This paper reports on the outcomes of a study into the reasoning and argumentation skills of pre-service education students engaged in problem solving within a computer-based learning environment. The implications for the design of a support framework to assist in this process will also be discussed.