Learning about complex and challenging science topics with advanced learning technologies requires students to regulate their learning. The deployment of key cognitive and metacognitive regulatory processes is key to enhancing learning in open-ended learning environments such as hypermedia. In this paper, we propose a metaphor - Computers as MetaCognitive tools - to characterize the complex nature of the learning context, self-regulatory processes, task conditions, and features of advanced learning technologies. We briefly outline the theoretical and conceptual assumptions of self-regulated learning (SRL) underlying MetaTutor, a hypermedia environment designed to train and foster students' SRL processes in biology. Lastly, we provide preliminary learning outcome and SRL process data on the deployment of SRL processes during learning with MetaTutor.