The Prime Focus Spectrograph (PFS) is a wide-field, multi-object spectrograph accommodating 2394 fibers to observe the sky at the prime focus of the Subaru telescope. The software system to operate a spectroscopic survey is structured by the four packages: Instrument control software, exposure targeting software, data reduction pipeline, and survey planning and tracking software. In addition, we operate a database system where various information such as properties of target objects, instrument configurations, and observation conditions is stored and is organized via a standardized data model for future references to update survey plans and to scientific researches. In this article, we present an overview of the software system and describe the workflows that need to be performed in the PFS operation, with some highlights on the database that organizes various information from sub-processes in the survey operation, and on the process of fiber configuration from the software perspectives.
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