A system and a method for dynamically optimizing an instrument system workflow based on operational monitoring and managing of a workflow for a hardware system. The system includes instrument resources and sample chambers, each resource and chamber with a dedicated sensor configured to acquire data. The system further includes a computing device communicatively connected to the instrument resources and sample chambers. The computing device includes a software application or program comprising a workflow builder, an execution engine, an analytics engine, a virtual system modeling engine, and an optional machine learning engine.