V4 code release: faster gene track rendering

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Tuesday, May 29, 2012

With the Start of Summer, we release our 4th version of Wash U Epigenome Browser. Following is a summary.

Major improvement

The Browser response is made faster by the new gene track. To render a gene track, only one Ajax query is needed to fetch the gene data. In the past two Ajax queries were needed and dragged down performance. A lot of coding work has been done for this, basically replacing the old design with the new one. Clear-looking arrow marks indicate strand of the gene. The marks are drawn both over introns and exons:

V4 code release- faster gene track rendering 0 1.png

Minor improvements and changes

To show more information about a gene, click on it to invoke the tooltip:

V4 code release- faster gene track rendering 1 1.png

In the balloon, gene symbol is printed in large italic font at top left. On its right is the "internal identifier" related to this gene track, and the link to the entry of this gene in an external database from which the gene info are retrieved.

In the middle of the balloon, click "show gene structure" to reveal the data on this gene:

V4 code release- faster gene track rendering 2 1.png

We are going to add the Gene Ontology annotation for all the species, and that will be represented in the same style as gene structure data here. The small static tooltip balloon is turning into a dashboard with rich information.

Also at control panel, some more functions are added to allow user to more conveniently control appearance of genomic feature tracks. Go to "Tracks" > "Genomic features" to see the contents:

V4 code release- faster gene track rendering 3 1.png

This table shows your collection of genomic feature tracks. You all know what the wrench icon does. Click it to configure the track's rendering through the panel displayed in floating toolbox. A few color boxes are also available on the right, which are shortcuts to the color configuration function. Click them will invoke the color palette:

V4 code release- faster gene track rendering 4 1.png

❖, ☁, and T are for "bigBed" tracks (e.g. genes or repeats), controlling color of "item box", "density plots", and "name text" respectively. The numerical tracks like "vertebrate PhyloP" has different shortcuts, "+" and "-" controls plotting color of positive/negative values. Hope you'll like them!

V4 code release- faster gene track rendering 5 1.png

      • notice to Maize genome users ***

We have changed the chromosome names from "n" to "chrn", where "n" is one of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Mt, Pt, UNKNOWN. We previously follows what maizesequence.org is using on their site, but we were persuaded to change into the "conventional style" (chr1 instead of 1). It is important to be aware of it as you need to prepare your bigWig/bigBed/BAM files accordingly so that they can be properly displayed on the browser.

Bug fix

Small coding error leading to erroneous display of some aradidopsis and maize genes is fixed. Now the genes are displaying alright:

V4 code release- faster gene track rendering 6 1.png