A biological sample analyzer, and a method and system for operation thereof, wherein instrument systems used to perform an assay of each of the biological samples loaded into the analyzer are operated in accordance with a schedule developed by a scheduler routine. The scheduler routine determines a time allowance for performing operations by instrument systems for conducting an assay on each biological sample from a load list indicating the type of assay to be conducted upon each biological sample. The time allowance determined is adapted to accommodate variations in actual performance of instrument system operations on each sample so that the assays of the biological samples can be performed by the instrument system operations in accordance with a reliable and reproducible schedule.
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