geWorkbench

Sequence Panel

• Add check box that allows displaying only activated sequences.
• Clicking on a line should display the sequence on a separate panel (as is the case for the promoter panel)
• A toggle bulb button should allow the user to see a portion of the sequence when mousing over the sequence, a certain number X of characters left and right of the sequence character when the mouse is over.

Project Panel

Saving a workspace using serialization makes the workspace irrecoverable from a subsequent application build. Another solution is needed.

FASTA format

• Keep track if something is a DNA or protein sequence: the later should not be amenable to promoter discovery.

Synteny

Go over this component and look in detail at how it works. E.g., the application seems to be freezing when selecting a marker, right-clicking in it and selecting "Add marker". What ever happens there should be probably handled on a separate thread.

Server side jobs

When starting a BLAST search (or similar) a results node is immediatelly added to the project folders, even as the job is still computing. Such nodes should be displayed with some visual cue indicating that they correspond to ongoing computation. Also, a user should be able to register an e-mail address where to be notified when a long running job is finished.

Panels

• Allow creating a new panel that contains the intersection or union of all markers (arrays) in a collection of selected marker (phenotype) groups.

SOM Viewer

• Allow a text box where to enter the name of a marker, hit <Return> and see the SOM cluster containing the marker.
• Highlight all SOM clusters containing markers from activated panels.

Structure Function

Add JMol.

Misc

• Enable the mechanism to export dataset nodes into multiple formats.