The goal of this research is to develop a comprehensive and holistic framework focused on fostering students’ scientific inquiry and research activities through scientific computing education by implementing computational experiments and simulations. The main scientific contribution of this article is a systematic approach to interdisciplinary and integrated curricula for Science, Technology, Engineering and Mathematics (STEM) education. The key interest is how to develop and apply appropriate learning resources that include software learning objects. In order to implement the goal of the research, we consistently study the problematic of developing the Technological, Pedagogical and Content Knowledge (TPACK) model for the scientific computing education domain and provide a methodology for the development and integration of relevant educational resources into the educational process. Based on this, we provide a generalized model of scientific computing education focused on scientific inquiry and research activities of students.