v16: Quick load, animated zoom, and bug fixes!

The version 16 code release highlights several new features, as well as a bunch of bug fixes.

You can download our source code from our server or dropbox folder.

Quick loading of a genome

If you want to quickly load up a genome on the browser, use the "Quick" button on the genome logo.

By clicking this button will let the browser load up more quickly by not loading the default experimental assay tracks.

Animated zoom effect

By dragging on the chromosome bar under the genome heatmap, or clicking Zoom Out button, the browser will show an animated zooming effect.

Configure track height

A unified method is now available to control track height through out the browser:

Right click on a numerical or categorical track and select Configure:

In the control panel, use +/- buttons to increase or decrease track height. You might need to click for multiple times to reach the desired height:

You can unify the heights of a group of tracks. To see that, right click in metadata color map where a color block spans across multiple tracks:

An extra button "Unify" appears. Clicking it will bring the heights of this group of tracks to a "consensus height":

Change color setting in metadata color map

Click on none-gray area on metadata color map and choose "Change color" option, following panel will appear to let you configure the colors:

BUG FIXES

Custom track and data hub are now correctly displayed in split panels.

Rearranging chromosomal order in Circlet graph now works correctly.


Wrong display on Firefox and Safari browsers have been fixed.

v15: search for tracks, search for KEGG pathway

Version 15 of WashU Genome Browser enables you to search for tracks by keyword. In the case of human, mouse, fruit fly, you can easily identify your target experimental assay tracks from our vast collection.

With help from KEGG support team, we've brought back KEGG pathway query. For all genomes hosted by our Browser, user can search for pathways curated by KEGG with keyword, and run Gene set view by selecting a pathway.

To get the source code of this version use the links below:
https://www.dropbox.com/sh/kyosquasf4rr4f4/QShHggjiKx
http://epigenomegateway.wustl.edu/info/source/subtleKnife.v15.tgz

Track search

To search for tracks by keyword, go to the small Toolbox panel and click "Tracks", then "Experimental assay tracks", the native track selection panel is shown.

Enter keyword in the text field on top of the panel and press  to get a list of experimental assay tracks matching your query:

Keyword is case insensitive. If you enter "dnase hypersensitivity" and it will be treated as one keyword.

Track either matching by name or description will all be shown. In above example, we intend to search for "DNase hypersensitivity" tracks but the first one is an RNA-Seq track, that's because the detailed information of this track contains the word "DNase".

To performed a search by combining multiple keywords, use AND operator (you must use upper case but not lower case "and"):

KEGG pathway

At toolbox panel click "Apps" then "Gene set view" to open this panel:

Click the button "KEGG pathway" to show the options:

Search for keyword "glyco" will get following hits for the human genome:

Each green button is one pathway, select one and click to launch gene set view with it:

After you run gene set view on the human glycolysis pathway genes, a table is displayed showing list of genes in this pathway. Gene name are in a blue button where the width of dark fill indicates the length of this gene in respect to the whole set. In this case gene "HK1" is the longest.

v14: alternative gene models viewing and selection

The version 14 of WashU Genome Browser provides a very useful feature related to handeling of alternative gene models. Please see below for details.

To get the source code of this version use the links below:
https://www.dropbox.com/sh/kyosquasf4rr4f4/QShHggjiKx
http://epigenomegateway.wustl.edu/info/source/subtleKnife.v14.tgz

Alternative gene models

Alternative gene model is prevalent phenomena in higher organisms. This screen shot shows multiple gene models of the human TP53 gene, as provided by two tracks:

Now if you use "Relocation" function of the Browser to relocate to TP53 gene, you have the option to choose which exact gene model you want to relocate to.

To see this, go to the Browser and show human genome, and click the blue button on the top of the page in the middle to show relocation options (if you're running Gene Set View, please quit to go to genome view to see this button):

In the second text box enter "tp53" then hit "Enter" or press :

A long list of TP53 gene models are shown. Click on one to select as destination for relocation. You can notice following points that aim to help you better visualize the differences between models:

1. structure of each model is plotted;
2. the widths of the graphs are proportional to the bp length of each model;
3. the models are aligned to indicate their relative position on the genome. In this case all of the TP53 gene models are from an interval (7565096-7590868) in chromosome 17.

Such handy function is also made into Gene Set View function as well. After you submit a set of genes, the gene list is displayed in the control panel with a green button for everybody:

Click the  ⇄  shows the list of gene models belonging to the queried gene in same fashion:

By selecting a model that entry in the gene set will be updated to the coordinate of your choice.

Bug fix and minor improvements

In the Gene Set View panel, the Choosing flank size options is back for gene set editing. We're still working to bring back the KEGG pathway query function.

An error associated with Zebrafish chromosome representation was fixed. This problem caused no chromosomes to be displayed in the relocation panel.