BioPAT® MFCS/win functions as a true SCADA system for reusable and single-use bioprocess applications. The software package also makes it possible to trigger different actions automatically based on events (e.g., initialization of substrate feed control after automatic batch end detection) to create a reproducible and automated batch process. BioPAT MFCS/win allows bioprocess operators to mirror steps of the process by selecting customized recipes that comply with the ANSI/ISA-88.01 standard for computerized batch control. The software system allows semi or fully automatic operations and state or time-dependent transitions.