geWorkbench

geWorkBench Component List and Status

Core Components (bundled with main application)

Major Components

• Microaray Panel
• Analysis (Hierarchical Clustering, SOM, T-Test, Multi T-Test)
• Filtering (Deviation, Affy detection call, Expression threshold, Genepix Flags, Missing values, 2 channel)
• Normalization (Housekeeping, Log2 transform, Marker based centering, Mean variance, Array based centering, Missing value, Threshold, Quantile)
• Expression Value Distribution
• Scatter Plot
• Tabular microarray
• Volcano plot

Minor Components

• Dataset Annotation
• Dataset history
• Experiment info

Additional Components (that pass the Plugin certification checklist)

• Reverse Engineering (should perhaps be broken into seperate components)
• Sequence retriever
• Cytoscape

Components that do not yet pass the Plugin certification checklist

• Associations (Interface needs to be standardized)
• caScript (Not yet complete)
• Synteny parameters (Does not generate proper dataset subnodes)
• Synteny main panel (Does not receive proper dataset subnodes, function not clear)
• Marker Annotations ("Retrieve Annotations" button should be disabled until user makes marker selection)
• Color Mosaic ("Pat" and "Abs" buttons appear to do nothing)
• Expression Profiles (Performs large computations on event reception and tab selection)
• caBIO Pathways (Function not tied properly to datasets, operation not clear)
• Go Terms (Interface not clear, needs to be standardized)
• GSEA (Contains 200+ megabytes of additional data)