Given the central place IT-based research tools take in scientific research, the marginal role such tools currently play in science curricula is dissatisfying from the perspective of making students scientifically literate. To appropriately frame the role of IT-based research tools in science curricula, we propose a framework that is developed to understand the use of tools in human activity, namely cultural-historical activity theory (CHAT). Accordingly, IT-based research tools constitute central moments of scientific research activity and neither can be seen apart from its objectives, nor can it be considered apart from the cultural-historical determined forms of activity (praxis) in which human subjects participate. Based on empirical data involving students participating in research activity, we point out how an appropriate account of IT-based research tools involves subjects’ use of tools with respect to the objectives of research activity and the contribution to the praxis of research. We propose to reconceptualize the role of IT-based research tools as contributing to scientific literacy if students apply these tools with respect to the objectives of the research activity and contribute to praxis of research by evaluating and modifying the application of these tools. We conclude this paper by sketching the educational implications of this reconceptualized role of IT-based research tools.