v6 release - major bug fix

This code release comes with major bug fix. Please go to the source code archive on our server or Dropbox to download.

Bug fix

When the Browser was showing data at basepair level, the use of coordinate was wrong at multiple places:

1. requesting data for the genomic region exposed by panning
2. placing the blue square box indicator on the small chromosome ideogram on the top left of the page
3. on obtaining genomic sequence for the region under view

Now these problems that were visible to us have been fixed. If you notice any more, comment on our blog and let us know!

Minor improvements

Y axis scale can now be drawn in genome heatmap:

To show the scale, increase track height to 20 or more pixels and the scale will draw automatically on the left side of the canvas.

And here's a slight improvement on the control panel. At "Heatmap track" panel, contents for "Data sets" and "Configure track selection panel" have been re-styled as "tab-page". Click any of the two buttons at top of panel to see:

This tab-page style is also applied to Bird's eye view panel.

Finally, we start depositing our source code archives into a dropbox folder which is publicly accessible. I guess this serves a nice fallback in case tornado strikes our server room and demolishes the servers. The user manual however is not included in the archive anymore to shrink size as there's only a scant 3GB space with my account so it needs to be lean (besides Xin hasn't updated his user manual since stone age).

v5 release - gene indicating function

Version 5 of Wash U Browser is available now. Follow this link and obtain the source code: http://epigenomegateway.wustl.edu/source/

New features

Sometimes the genes can only have parts but not the whole displayed in genome browser. For example when viewing a short interval centering over transcription start sites of genes in Gene Set View:

Genes in the gene track are partially displayed in above view. As a result it would be difficult for user to view the gene's entire structure unless he/she quits Gene Set View and relocates to this gene.

Now this problem is solved with the gene indication function. You only need to click on this gene to invoke the tooltip balloon and it will show you:

On the top of balloon, a small graph is drawn to display the gene in its entirety. As usual, the thin lines indicate introns, thick blocks are exons, and the smaller blocks at each end are untranslated regions (UTRs). A yellow box marks the part of the gene that's currently visible in the gene track.

Size of this graph is constant, it won't change with the actual length of the gene or balloon size. And the graph won't show up for genes completely displayed in the track. Currently there's no clickable function attached to this graph, but I wonder if user will find it useful to be able to control the plotting color by clicking it? Anything else?

Like I promised, the gene tooltip balloon is turning into a fully loaded dashboard. More interesting and useful functions will be added here to let you know, recognize, study, and operate the gene under your focus. Hang on with us!

Bug fixes

1. Imprecise gene placement in the gene track during gene set view is fixed
2. Imprecise indicator (blue rectangle) placement over small chromosome ideogram on top left corner of the page is fixed.

v4 code release: faster gene track rendering

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:

Minor improvements and changes

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

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:

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:

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:

❖, ☁, 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!

*** 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: