Protocol framing identifies the biological question, research stage, endpoint, sample or dataset, intended interpretation, classical reference, and stop criteria before acquisition or simulation begins. Calibration, background, temperature, preparation, batch effects, blinding, preprocessing, repeatability, and multiple testing are treated as competing explanations that the evidence must address.
The same framing states whether the work is fundamental measurement, analytical validation, preclinical research, or part of a separately sponsored clinical programme. Consent, lawful use, minimum necessary data, access, retention, de-identification, linkage, and population limits remain part of the research record rather than assumptions hidden behind the analysis.