Enhanced track information display

An enhanced display of heatmap track information is now available. To use it, right click on genome heatmap to invoke context menu and select "Information" option:

A panel will appear in floating toolbox showing the track information:

You can see information are now categorized for display. On show is the "general" category, in this case are general info that are retrieved from GEO website.

Second category is data processing parameters and stats. Usually we can't just take the processed data as granted but we have to look into the way it was generated to see if it make any sense at all.

Next category is "Other versions". Right now there's nothing, but we are re-processing the Roadmap and ENCODE data and you will be able to look at our versions as alternative when you are not satisfied with what's available from GEO.

Next category is link to GEO. If the track corresponds to an entry in GEO database, a button will be displayed here. Pushing the button will take you to there.

The last category is the juice, the real thing. However there isn't any contents at the moment, and you have to wait until we finish the re-processing. By then you will be able to look at detailed read alignment for any sequencing tracks available on our browser. 

Enhanced chromosome ideogram graph

This is about the small chromosome ideogram graph on top left corner of the page, not the ideogram graph beneath genome heatmap.

The graph always shows entire chromosome ideogram in which current displayed region locates. It used to be in fixed width. Now the width adjusts to page width. And a ruler is shown below it to mark out sequence length:

You can still drag on the ideogram graph to zoom into a region.


However when current displayed region spans multiple chromosomes, the graph will change into something like this:

Above shows a region spanning chr9 and chr10. Instead of drawing ideograms of chr9 and chr10 two hollow boxes are drawn. Beneath them shows approximate length of the two chromosomes.


And finally, when doing Gene Set View, the graph will be like following:

Where boxes with alternating fill color are used to indicate genes used in the View. Gene name is printed inside box whenever it fits in.

And enjoy the Spring Break!

Genome selector on page start up

Now when the browser is first started, the genome selection dialog box will be displayed. The loading process is paused unless a genome is selected.

This eliminates the nuisance of loading up human genome every time at start up while user's interest is something else.

Somewhat unified method to rearrange items in a list

As demonstrated above, a new function interface is in use so that you can manually rearrange things in a list. The function is extremely simple and intuitive, just a small panel with four buttons in it. Clicking  will move the item one level towards the head,   will move it one level towards the tail.  will move to the head and will move it to the tail.

This function is mainly developed towards compatibility with touch screen devices (and now I accept donations of touch screen mobile phones for software testing purpose - -|||). Click anywhere on the page to dismiss the panel.

It applies to following scenarios:

1. Rearranging single track in genome heatmap
2. Rearranging multiple tracks spanned by a color block in metadata color map (press cursor and drag on the color block still works)
3. Items in Gene Set View (that is horizontal order of items in genome heatmap)
4. Genomic feature tracks (that is when multiple genomic feature tracks are show, you can move one track towards or away from genome heatmap)
5. Scaffold sequence, both for displaying in genome heatmap, and in Bird's Eye View

Minor improvements to Gene Set View

In a word, you can visualize flanking regions when using Gene Set View:

Above screenshot demonstrates the case. The green/red portion at the ends of each item marks out flanking region added to the gene. Green for upstream and red for downstream (relative to the gene strand).

When you submit gene sets to run Gene Set View, you have the option to decide which part of gene to show in the View:

Options including "promoter+genebody", and "custom region" will have this effect.

Besides, the "custom region" option works on not only genes, but also on genomic coordinates. So you can add flanks to your genomic intervals:

Above is the example of running Gene Set View with genomic intervals instead of genes. The input is coordinates of a bunch of MER41B elements. Each is padded with 500 bp on both sides. I guess this makes a nice repeat browser? Well notice that although repeats do have strand information, but I'm using strand-less genomic coordinates as input, the upstream/downstream padding are irrelevant to actual strand of repeats.

Scaffold sequence configuration function

The "Contig View" function has officially retired - been replaced by the scaffold sequence configuration function where arbitrary and flexible choice of scaffold sequence can be chosen for display.

At control panel go to "Genomic view" --> "Scaffold sequence" to view the interface:

The table shows list of scaffold sequence currently in use, and their order of appearance on the horizontal axis of genome heatmap.

To add more sequences to the list, click "Add more" button, a new panel will appear:

The sequences have been grouped. In this case of human genome, two groups are shown in the panel, click to reveal list of items:

The "chromosome" group contains fully assembled chromosomes, and the "other" group contains anything else. Sequences are presented as clickable rectangles for you to select. Box filled in blue indicates the sequence is in display, and unfilled means it isn't and can be added.

To remove from display, click X button to mark for removal, the "Update" button will appear. Click button again to unmark. You can mark multiple sequences before clicking the update button to remove them:

If you click the chromosome name, or anywhere except the removal button, the sequence will be in bold face indicating it is selected. Only one item can be selected a time. More buttons will appear allowing you to move this item in the list:

Use arrow buttons to move selected item along the list. Once moved, you need to click "Update" button to take effect. Click the Knight button to show this sequence in its entirety.

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The Bird's eye view has identical scaffold configuration function, available from the Bird's eye view panel (click button Configure and then select "scaffold sequence"):

An identical looking panel will appear:

There you can configure scaffold sequences to be used in Bird's Eye View, which is totally independent from what is used in genomic view.

And that's it. This function replaces the cluttered design of Contig View, and is the first step towards building the Repeat Browser -- where over 1000 repeat subfamilies are available, and user needs to be able to browse and select them in an intelligent manner (following Class > Family > Subfamily hierarchy is essential instead of looking through a huge list).