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The implementation of bioassays in pin-constrained biochips may involve pin-actuation conflicts if the concurrently implemented fluidic operations are not carefully synchronized. We propose a two-phase optimization method to identify and synchronize the fluidic operations that can be executed in parallel. The goal is to implement these fluidic operations without pin-actuation conflict, and minimize the duration of implementing the outcome sequence after the synchronization. The effectiveness of the proposed two-phase optimization method is demonstrated for a representative 3-plex assay performed on a fabricated pin-constrained biochip.