Oscillations are a common feature throughout life, forming a key mechanism by which living systems can regulate their internal processes and exchange information. To understand the functions and behaviours of these processes, we must understand the nature of their oscillations. Studying oscillations can be difficult within existing physical models that simulate the changes in a system’s masses through autonomous differential equations. We discuss an alternative approach that focuses on the phases of oscillating processes and incorporates time as a key consideration. We will also consider the application of these theories to the cell energy metabolic system, and present a novel model using weighted nonautonomous Kuramoto oscillator networks in this context.