Aspects of the present invention relate to an automated cell culture instrument and to methods for operating such an instrument. In one aspect, the cell culture instrument includes a computing unit and a plurality of electrically controllable resources (e.g., sensors, actuators, etc.). The computing unit receives a protocol, schedules the resources so as to execute the protocol, and operates the resources as scheduled or in response to so as to provide an improved environment for cell culture growth. The computing unit may simulate protocol execution in connection with the scheduling or execution of the protocol.