1. A flexible instrument control and data storage/management system for representing and processing an assay plate having one or more predefined plate locations, the system comprising a non-transitory computer readable medium device including a software architecture that performs the steps comprising: (a) accessing a database comprising a plate type directory including a plurality of graph data structures representing the physical structure of said assay plate, wherein said graph data structures each comprise a node for each of the one or more predefined plate locations, and said node is hierarchically arranged to correspond to the physical structure of the assay plate; and (b) accessing at least one layer object that maps at least one data object to one or more nodes within a particular graph data structure, wherein said at least one data object comprises one or more data records, wherein the at least one data object is not stored on said database comprising the graph data structure and wherein the assay plate has a predefined number of wells arranged in a plurality of well groupings, and wherein the one or more predefined plate locations include: one or more spots in each well; and one or more sectors associated with each grouping of wells, wherein the one or more sectors each contain the one or more spots, respectively, from each well of the associated group of wells.