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Bifocal Modeling (BM) is an approach for science learning that links students’ physical experimentation with computer modeling. This study is among the first implementations of BM in a classroom setting and it seeks to understand to what extent it could be tailored to beneficially complement a traditional teaching. The study utilized two groups of 50 9th grade students; one assigned to BM, whereas the other served as control group receiving a traditional science class. Results indicated that students who participated in the BM group showed significant improvement in their understanding of the content and meta-modeling knowledge. As part of this study we also developed a rubric for assessing model-based reasoning on the basis of student drawings.