This working paper proposes two conceptual tools for examining emerging research systems. Specifically, the paper highlights Khaldunian theory of cyclical change to incorporate the ever-changing nature of global research and knowledge production, and an agential lens that provides analytical space for examining actors in the continuously changing global system. Agency in the global research space operates at multiple scales and contributes to the rise and decline of knowledge production paradigms, resembling that of cyclical change discussed in the main body. These conceptual tools can be useful lenses for researching the global research system and cross-border research collaborations but are not exhaustive. The working paper provides a discussion on future research directions to illustrate the potential use of these conceptual tools in upcoming projects.