Abstract: A controller for an automated immunoassay system is provided to manage the system resources and control the flow of samples under test. The controller allows tests to be run dynamically instead of in a serial, first in first out flow. The controller evaluates the set of tests to be run and generates a sequencing strategy. The sequencing strategy is based on the paths specified for each type of assay, the numbers of tests to be run, the priority of each test and the resources required for each test. In addition, the controller can resolve resource allocation conflicts and modify the sequencing strategy as test conditions change during operation.