Improving students' STEM competencies is important and relies on fine-grained assessments, however, assessing scientific inquiry in an authentic, automated way is challenging for a number of reasons. Here, we provide an overview of how the learning sciences and computational sciences were used in the design and development of Inq-ITS and its alerting dashboard, Inq-Blotter, which are used to: 1) assess students' competencies in real time, 2) drive a pedagogical agent to scaffold students' inquiry in real time, and 3) generate teacher alerts and TIPS in real time to support instruction. This work reflects advances in several areas including science cognition, performance assessment and intelligent tutoring systems for science, as well as teachers' instruction of science. Due to these functionalities, systems like Inq-ITS will eliminate the separation between learning activities and assessment activities, realizing the long-range vision for both technology-based environments and reform policies like NGSS and 21st century skill frameworks. See inqits.com/research to learn more about how Inq-ITS was developed as well as some of our latest findings demonstrating students' and teachers' success with Inq-ITS.