Vascular calcification, a prevalent and progressive disorder, involves numerous interactive, autocrine, paracrine, and endocrine regulatory mechanisms and is thus ideally suited for analysis using a systems approach. This approach focuses on creating quantitative, testable models of complex biological systems that take into consideration the time dimension. They are usually expressed as mathematical models, and because of their time dependence and complexity, they usually require computer simulation to determine predicted outcomes. Here, we provide an example of such a model used to analyze self-organization and mineralization of vascular stem cells, using partial differential equations capable of accurately predicting experimental outcomes. Such systems-based models are useful in many aspects of cardiovascular medicine.