Inquiry-based modeling is essential to scientific practice. However, modeling is difficult for novice scientists in part due to limited domain-specific knowledge and quantitative skills. VERA is an interactive tool that helps users construct conceptual models of ecological phenomena, run them as simulations, and examine their predictions. VERA provides cognitive scaffolding for modeling by supplying access to large-scale domain knowledge. The VERA system was tested by college-level students in two different settings: a general ecology lecture course (N=91) at a large southeastern R1 university and a controlled experiment in a research laboratory (N=15). Both studies indicated that engaging students in ecological modeling through VERA helped them better understand basic biological concepts. The latter study additionally revealed that providing access to domain knowledge helped students build more complex models.