Thursday, December 27, 2012

v13: enhanced user interface, architectural overhaul

Happy Holidays to you all! We're very happy to announce a brand new WashU Epigenome Browser. Our goal is to make the User Interface rich in functionality, while keeping it as simple as possible.

Get the code here: from our server, or dropbox
v13 .tgz file does not include folders "images" and "manual", which are available through past version .tgz files

To use the URL parameter function, see instructions in this new post.

To use the datahub function, see instructions in this updated post.

Docs that are not available for the moment:
  1. new interface of scaffold sequence management, Gene Set View (management)
  2. simplified interface of Genome Snapshot (aka Bird's Eye View)
  3. new function: split panel display (for browsing long-range interaction data sets)
  4. improved Circlet View interface

Following screenshot is the part of Browser UI that you often see.

Old Browser is here in case you need to access your saved sessions. We will keep it alive for two months and alert you before we take it down.

Following is a quick overview of some new features available on the new Browser:

Toolbox as the "single entry point"

Please find the row of three buttons in the middle of toolbox: "Tracks", "CustomTK", and "Apps". This is the entry point to a majority of the Browser's functions.

Tracks refer to the collection of tracks that are available through the Browser service. Clicking on it shows a small menu which leads to the selection panel for each category of tracks:

CustomTK links to the panel for custom track submission and management. Number in the parenthesis is the # of custom tracks you've submitted.

Apps links to the list of applications.

Genome navigation

On top of Browser panel a blue button shows the current coordinate. Click this button to show options to relocate:

Or as indicated, click the button in this small panel to visually select a new region from one of the chromosomes:

Agile track handling
The track labels are always shown on the left of the track images, mouse over the label for complete track name and more info (e.g. color scale bar for the heatmap quantitative tracks)

Press your mouse on the track header and drag it up or down, the track will be rearranged accordingly. You can even drag the heatmap track outside of genome heatmap, or bring a track into the genome heatmap from outside. You're in full control now:

Handy sticky notes
A small but perhaps very useful new feature is the coordinate-anchored sticky notes. It's incredibly easy to use. Just right click on the chromosome ideogram below the genome heatmap, and an input panel appears:

Once a note is made, it is attached to a point in the genome and is indicated by a "note" icon. You can save notes in Session so they are persistent, give it a try!

A few things are still missing here, but we're working to bring these functions back as soon as possible:
  • Pairwise comparison and hypothesis test over quantitative track data
  • Querying and retrieval of KEGG pathway
  • SVG output for Genome Snapshot and Circlet view (previously known as Henge View)