Systems, devices, and methods for encoding digital representations of musical compositions are described. Various components of a musical composition that are defined in modern music theory, such as notes and bars, are encoded as respective hierarchically-dependent data objects in a data file. The hierarchically-dependent data objects encode the musical composition in a tree-like data structure with modular nodes and adjustable relationships between nodes. Note start times and beat start times are encoded independently of one another and characterized by a timing relationship that captures the expressiveness imbued when notes and beats are not precisely synchronized. Musical variations that preserve the timing relationship between the notes and beats of the original composition are also generated and encoded.