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org.biomage.Array: Javadoc index of package org.biomage.Array.


Package Samples:

org.biomage.Array
org.biomage.ArrayDesign

Classes:

ArrayDesign_package: Describes a microarray design that can be printed and then, in the case of gene expression, hybridized. An array design consists of several features (also called spots) in which reporter sequences are placed. Many features may have the same reporter replicated and a reporter may be specified in one or more array designs. The nature of the reporter's biosequence placed on a spot will depend on the technology. Two well-known technologies differ significantly-spotter arrays draw material from a well and place a spot on the array whereas in situ oligo arrays are created through the synthesis of many, ...
ArrayGroup: An array package is a physical platform that contains one or more arrays that are separately addressable (e.g. several arrays that can be hybridized on a single microscope slide) or a virtual grouping together of arrays. The array package that has been manufactured has information about where certain artifacts about the array are located for scanning and feature extraction purposes.
Array_package: Describes the process of creating arrays from array designs. Includes information on how arrays are grouped together, if relevant, how an array deviates from its array design both in layout and per feature and potentially contains references to LIMS data that might contain more detail on the BioMaterial used to create the reporters.
ArrayDesign: Describes the design of an gene expression layout. In some cases this might be virtual and, for instance, represent the output from analysis software at the composite level without reporters or features.
DesignElementGroup: The DesignElementGroup holds information on either features, reporters, or compositeSequences, particularly that information that is common between all of the DesignElements contained.
ArrayManufactureDeviation: Stores information of the potential difference between an array design and arrays that have been manufactured using that design (e.g. a tip failed to print several spots).
Fiducial: A marking on the surface of the array that can be used to identify the array's origin, the coordinates of which are the fiducial's centroid.
ZoneGroup: Specifies a repeating area on an array. This is useful for printing when the same pattern is repeated in a regular fashion.
PositionDelta: The delta the feature was actually printed on the array from the position specified for the feature in the array design.
ManufactureLIMS: Information on the physical production of arrays within the laboratory.
PhysicalArrayDesign: A design that is expected to be used to manufacture physical arrays.
Array: The physical substrate along with its features and their annotation
CompositeGroup: Allows specification of the type of Composite Design Element.
ReporterGroup: Allows specification of the type of Reporter Design Element.
ManufactureLIMSBiomaterial: Stores the location from which a biomaterial was obtained.
ZoneLayout: Specifies the layout of features in a rectangular grid.

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