WC-Rules is a formalism for describing composite, mixed-grained, multi-algorithmic WC models. WC-Rules provides modelers a high-level, biologically-intuitive language for describing models in terms of patterns of metabolite, DNA, RNA, and protein species and rules for their interactions. Together, these species patterns and interaction rules enable modelers to describe the molecular complexity of any biochemical process including metabolism, replication, transcription, translation, and signaling. WC-Rules can also record the provenance of models including their data sources and assumptions.