Figure 1

BASE data layer overview. The main theme of a microarray experiment is captured in the lower part of the figure where the Experiments module groups BioAssays into a logical unit and keeps track of analysis made within the experiment. The Experiments are connected to RawData and physical experimental steps like Hybridizations. The Hybridization objects connect the array information (ArrayDesign, ArraySlide, ...) with biomaterials (LabeledExtract, Label, Sample, ...), and all array production and biomaterial handling is tracked providing a LIMS system for arrays and biological material. The upper part of the figure shows many objects needed to support the basic microarray experimentation flow; the Reporter module provides information about probes on an array, Annotaions provides annotation information to basically any item in BASE, Quota handling, and Plugins & Job handling for running analysis on a cluster of back-end computers. These utility modules are connected with the lower part modules but these connections are excluded in the figure to avoid clutter. For further details on the different modules and interconnections please read the developer documentation available at the BASE web site http://base.thep.lu.se.