This paper demonstrates a methodology for effectively integrating computer-based learning tools in science teaching and learning. This methodology provides a means of systematic analysis to identify the capabilities of particular software tools and to formulate a series of competencies relevant to physical science that could be developed by means of these capabilities. This analysis could inform the transition to technology-rich learning environments by helping to deflect reliance on computer-based tools for objectives they cannot meet, while encouraging the design of activity sequences that make the most of the educationally useful capabilities of available computer-based tools. This methodology is demonstrated by means of two software tools widely used in science learning, namely modelling and simulation tools. (Contains 1 figure, 2 tables, and 10 notes.)