The Virtual Telescopes in Education (VTIE) project, is providing tools for teaching astronomy in K-12 classrooms using remotely controlled telescopes. VTIE's main goal is to promote scientific literacy, including a conceptual understanding of the physical world and the scientific process itself. This paper describes an essential component of VTIE: the scientific investigation system for telescopes in education research (SISTER). Students are aided in the preparation of their observing proposal by a glossary tool for dynamically inducing hyperlinks tailored to a student's reading level, a proposal generation interface to guide them through the process of formulating a scientific question, and a paper writing tool to report the results of the analysis of the data. In this paper we present the architecture and methodology for SISTER.