v22 (3 of 3): better track search, and information display

Track search

You can quickly find track using the track search. On browser, click "Tracks" and find the search box:

Enter keywords and press "Search" or hit Enter. To use multiple keywords, join them by "AND".

The search will turn up not only experimental assay tracks, but annotation tracks (e.g. genes or repeats), and tracks from your datahub or custom tracks. Track must be labeled with corresponding keyword or annotated using a matching metadata term to be found out.

Track information display

To see information of a track, right click and select Information:

Track information will be shown as various categories:

Gray boxes in the top row are metadata terms used to annotate this track. Click a term to show its hierarchy in the controlled vocabulary:

v22 (2 of 3): public datahubs

From version 22 the browser is now equipped with "Public Datahubs", which are in-house curated datasets that contain publicly available assay results of high scientific value and interest to the research community. The Public Hub is in the form of datahub, which is independent from the browser track database, and can be hosted on any web server on the Internet.

A pilot release of Multiple Myeloma genomics sequencing results is available as an hg18 public hub in the human genome. The data is provided by James Bradner's lab at Harvard Medical School.

To see the public hub listing for a genome, click "Track", then "Experimental assay tracks". The Experimental Assay Track panel will be shown. Click tab "Public datahubs" to show the listing:

We would love to publish your data! Please feel free to contact us at epigenome@lists.genetics.wustl.edu

v22 (1 of 3): call super enhancer using ROSE

We release version 22 of our Browser with the first integrated app: ROSE-the super enhancer calling tool. You can find applications of ROSE in these two papers from the Cell journal:  Loven, J. et. al. and Warren A. et. al. You can get the source code of ROSE from bitbucket.

This work is done in collaboration with Dr. Charles Lin from James E. Bradner's lab at Harvard Medical School.

Call super enhancer with ROSE

At the time of writing, ROSE can be used for following genomes: hg18, hg19, mm9, rn4, dm3, danRer7.

Follow these steps to submit a "call super enhancer" job.

1. Open the browser and display one of the supported genomes.

2. Upload a set of transcription regulator binding regions that you would like to check for existence of super enhancers. The binding regions must be submitted as a gene set. Most easy way is to upload them from a tabular text file.

3. Submit a custom BAM track containing read alignment data from the transcription regulator ChIP-Seq experiment. Optionally you can submit a ChIP-Seq Input track, from which the "background" will be subtracted.

4. Click "Apps" then "Call super enhancer". The ROSE interface will be shown as in the following screenshot:

5. Assign binding sites, BAM track, and enter your email address in the form. Click "Submit" button to run the job. Once the job is submitted, you can close this panel and continue using the browser. After a short while our server will finish processing your job and will send you an email with the key to retrieve results.

The amount of time is heavily determined by number of binding sites you submit. Typically less than 10min for 5000 binding sites in human genome. Also the server load level will also impact the speed of job processing.

6. Retrieve job with your key. When the job is successfully processed, you can either download the results as a compressed file archive, or visualize it:

Following screenshot shows the "Call super enhancer" results visualized as an interactive scatterplot, where top ranked dots are super enhancer candidates. You can also display super enhancers as bed track by click the button on top of the graph:

v21: Creating and managing multiple gene sets

Version 21 features the all-new gene set creating and management functions.

Create a gene set

Click the "Apps" button, then select "Gene set" option to see following panel:

Click the "Add new gene set" button:

To use the default list of genes, simply click Submit button, a new gene set will be added:

To add additional gene sets, click the Add button again. Let's try "BED file" option this time:

You can upload a BED file and get a "gene set" with all the regions in the file. In fact, you have freedom to use any format for your text file, not restricted to BED or GFF or whatever. You only need to specify column index of required fields to load it.

Once a text file is loaded, it will be shown as a second entry:

Additionally you can query and load a KEGG pathway as the third method.

Manage/edit a gene set

Click (left-click) on a gene set entry to get available options:

Choose the first option "View and edit" to get following panel:

As indicated, you can use options in this panel to edit this gene set, including re-ordering, switch gene model, mark and delete items, add new items, change flanking regions, and rename this set.

Click button Done to hide the editing options.

Run gene set view

Click a gene set and choose Gene set view option:

The browser will run Gene set view using the genes or coordinates in this gene set. To quit Gene set view, click the "Turn off" button pointed by the cursor in the screenshot:

Note: to add flanking regions to the gene set view (or to add/remove items and such), you need to perform edit to the gene set, then re-run Gene set view using the updated set.

Use gene set in other apps

You can choose a gene set and send it to any other appropriate apps. Simply click the gene set and choose the option that corresponds to the desired app. From the app's configuration panel (if available) you can also find the option to choose gene set.

Extra: gene sets from datahub

You can put a gene set in your datahub descriptor file. Click this link to see the sample hg19 datahub now hosting two gene sets:

http://vizhub.wustl.edu/hubSample/hg19/hub2.txt

Click this link to display this datahub and load the gene sets defined in this hub (go to Gene set management panel to check it out):

http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub=http://vizhub.wustl.edu/hubSample/hg19/hub2.txt

The sample hub file contains description on how to write a gene set. Very simply, just enclose your gene set inside a pair of keywords: genesetstart and genesetend. The browser will try to use all contents between this two keywords as a gene set.

This makes sure that your gene set will always be there unless you change it, because it doesn't rely on session database to store.



Finally a few notable points:

1. All your gene sets can be saved in a session (and recovered by it).
2. By contrast, with URL parameter you can only keep one gene set.
3. You can save multiple gene sets with a datahub (but you need to put it on the web).
4. When a gene set is sent to an app (e.g. Gene set view), it duplicates a copy of itself and is separate from the set that is running the app. So if you modified the gene set, the change will *not* be automatically reflected in the app, but you need to re-submit the gene set to the app again to get updated results.
5. Gene Set View operation panel is no longer around.
6. Due to some hard changes with the new gene set function, sessions with Gene set view saved prior to Version 21 release might not be correctly recovered. We apologize for any inconvenience! We recommend the use of datahub to encode gene set which should be both stable and convenient.

You can get the source code from dropbox, or our server.

A very brief list of steps to install mirrors of our Browser is now available. It is rather sketchy and imcomplete and we will try to improve it.

v20 (3 of 3): refresh cache of custom tracks

When you have some custom tracks displayed on the Browser, and you updated the track files, you need tell the Browser to refresh cache of the updated track, so that it can be correctly displayed.

To refresh cache of custom tracks, click "CustomTK" button on the top of browser and find the button  (this button will only be shown when custom tracks have been submitted):

Click the button to open a new panel:

Choose tracks that need to be refreshed by clicking the track box, then click button to refresh the cache. You can select multiple of tracks and submit. Do not hide this panel while the server is working.

When the cache is refreshed, the track will be marked by a green tick. Upon any error the track will be marked by a red cross:

After the cache has been successfully refreshed, you can resume browsing by closing this panel.

v20 (2 of 3): embedding browser

Created: 2013/7/5
Last updated: 2014/2/6


From version 20 you can now embed the WashU EpiGenome Browser in your website! You only need to do some trivial HTML and JavaScript coding to have it. The embedded browser is full-blown browser as the one running on our server, and you can customize it to a great extent to show your stuff in your own way. Best of all, it's part of your website.

Examples

http://cgs.wustl.edu/~xzhou/embed/1.html

This web page has a browser embedded in it. It automatically embeds the browser as soon as the webpage itself is loaded. It shows the default tracks from the Roadmap Epigenomics public hub on human hg19 genome.

http://cgs.wustl.edu/~xzhou/embed/2.html

This example loads human/hg19 genome and displays a set of custom tracks.

http://cgs.wustl.edu/~xzhou/embed/3.html

This example can embed browser according to user's actions (you need to click a button to embed a browser).

You can see the source code of these examples in the HTML files (1.html, 2.html, 3.html) and adapt them for your purpose.

How the first example works

1. add following lines in the <HEAD> section of your web page:

<link rel="stylesheet" type="text/css" href="http://epigenomegateway.wustl.edu/browser/style.css" />
<script type="text/javascript" src="http://epigenomegateway.wustl.edu/browser/base.js"></script>
<script type="text/javascript" src="http://epigenomegateway.wustl.edu/browser/personality.js"></script>
<script type="text/javascript" src="http://epigenomegateway.wustl.edu/browser/embed.js"></script>

2. call the function embed_washugb to embed a browser. Most simply it can be done with following lines of javascript:


<script type='text/javascript'>
embed_washugb({
host:'http://epigenomegateway.wustl.edu',
container:document.getElementById('container_id'),
genome:'hg19',
});
</script>

This example requires a <div> element with ID of "container_id" in the web page.

The embed_washugb function requires a hash object as its only argument. All customization will be done through contents of this hash, as explained below.

embed_washugb options

All parameter names (keywords) are in bold face and are case-sensitive.

host

URL of the hosting server
value: url string

container

DIV object in which the browser will be embedded. You can supply the object programmatically, or by the object's ID (document.getElementById('xxx'))
value: DIV object 

genome

genome name, e.g. hg19, mm9
value: genome name string

leftSpaceWidth (optional)

the width of space on the left of genome heatmap (where track names are shown)
value: positive integer

panelWidth (optional)

width of the genome heatmap panel
value: positive integer

noPanelwidthConfig (optional)

do not show browser panel width configuration button (gear button)
value: true (or 1 or anything evaluates to true in javascript)

noDeleteButton (optional)

do not show delete button (for deleting the embedded panel)
value: true

hideTrackName (optional)

do not show track name on the left of browser
value: true

hideChromNavigator (optional)

do not show the chromosome navigator on top of the browser tracks
value: true

hideTopRuler (optional)

do not show ruler on top of the browser tracks
value: true

hideMetadataColormap (optional)

do not show metadata color map
value: true

maxTrackHeight (optional)

maximum track height, this only applies for the automatic track height adjustment when the browser loads for the first time
value: positive integer

noDefaultTrack (optional)

do not load any default native tracks
value: true

showContent (optional, new parameter)

define contents to be displayed in the embedded browser
value: an array of objects, each object defines a track in the same fashion a JSON data hub is written.

v20 (1 of 3): dual genome display

The version 20 of WashU EpiGenome Browser sees lots of exciting new features, which will be talked about in 3 blog posts. Here we introduce the "dual genome display". Follow the links to see embedding browser, and custom track cache refreshing.

As usual, you can get the source code from our server or dropbox. A short guide has been written to help you install a local mirror of the Browser. Feel free to email us about problems.

The Dual Genome Display

Click genome logo on top of the browser page, to see a small menu showing up:

Click "Add new genome" option, the select-a-genome panel will be shown:

Suppose we choose mm9 by clicking the Quick button, a new browser panel about Mouse genome will be shown (beneath the original hg19 genome):

The newly added mouse genome can be navigated separately from the existing human genome. All the browser functions and apps can be applied on the mouse genome. Give it a try and have fun! When you are done, you can click the red X button to remove the mouse genome.

It's not limited to "dual" genomes only, you can add 3 or more genomes if you prefer.

You can show the same genome (e.g. all hg19) multiple times. In that case, the custom track information will be shared among all the browsers from the same genome.