Systems and methods for autonomous workflow management

A computer system, comprising:

• a hierarchical software architecture comprising a plurality of software layers that are collectively configured to automate processing of at least one object through a workflow process, wherein each of the plurality of software layers is configured to be ignorant to a functionality of another of the plurality of software layers, and wherein the plurality of software layers comprise:
• a first software layer of the plurality of software layers configured to guide the at least one object between one or more work cells during progression of the at least one object through the workflow process;
• one or more second software layers of the plurality of software layers, wherein each of the one or more second software layers are configured to manage execution of one or more steps associated with the workflow process in the one or more work cells;
• and
• one or more third software layers of the plurality of software layers, wherein each of the one or more third software layers are configured to manage execution of tasks, performed by an instrument of a plurality of instruments contained in the one or more work cells, in furtherance of the one or more steps.