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Study units are included in in a protocol specification using the StudyUnitControl. A StudyUnitControl references a study unit. A StudyUnitControl takes inputs and outputs. Inputs to a study unit might come from the study's archive. Outputs from study units might be deposited in the archive.
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Instruments are included in a protocol specification using pInstrumentControlInstrumentControl. pInstrumentControl InstrumentControl references an instrument. A pInstrumentControl An InstrumentControl takes inputs and outputs. Inputs to an instrument can include "preloads". Outputs from an instrument can include "critical data items" that figure into subsequent control constructs that play a role in the flow of instruments.