v30: custom gene tracks

All the gene tracks on the browser have been upgraded to a new format, and supported by a new mechanism. For all animal genomes all the gene track data have been updated with latest downloads from UCSC Genome Browser. A RefSeq genes and "xenoRefSeq genes" tracks are available for every animal genome and provides good annotation coverage, the latter provides homologous genes from other species.

This new gene track mechanism also supports custom gene tracks:

In above image two gene tracks are shown. The one on top is the native hg19 RefSeq gene track. The green track beneath it is an replica custom track. You can see from the details about this track in the menu box.

An example custom gene track can be found in this hg19 data hub, look for the word "hammock":

http://vizhub.wustl.edu/hubSample/hg19/hub.json


This page has some instructions about preparing gene tracks.

Download the browser source code from here or here.

v29 (4 of 4): the methylC track

Version 29 makes official unveil of the "methylC" track, though it has been available on our browser for a while.

The methylC track is able to display single-base DNA methylation data by discerning cytosine context (CG/CHG/CHH), strand-specificity, and incorporating confidence level data.

Thus it is excellent in visualizing whole-genome bisulfite sequencing (WGBS, or methylC-seq) results. In this case the confidence level data is read depth.

Surely it makes same support on Reduced Representation Bisulfite Sequencing (RRBS) results.

It can even be used for array-based methods such as Infinium 450K. In this case the -log10(P-value) will be used as confidence level.

Refer to http://epigenomegateway.wustl.edu/+/cmtk/ for more details.

A manuscript describing methylC track is under preparation.

v29 (3 of 4): delete custom tracks

We brought back a function that allows you to delete custom tracks in your current session.

After you've loaded custom tracks, click "CustomTK" > "List of all":

From the custom track listing you can find a "delete" button following each track. Click this button and the track will be gone, so be careful.

v29 (2 of 4): displaying track hubs from UCSC Genome Browser

From version 29 we make initial support of UCSC track hubs. However due to inconsistency problems the support is partial:

• bigWig and BAM tracks are supported
• VCF track is not supported for the moment
• bigBed is not supported
• information on all composite tracks will be merged into one metadata vocabulary
• only a handful of rendering controls can be parsed for the moment

To see public hub listing on UCSC, go to http://genome.ucsc.edu/cgi-bin/hgHubConnect

Copy a hub file URL (e.g. http://zlab.umassmed.edu/zlab/publications/UMassMedZHub/hub.txt) and enter it into the text field below. Choose "UCSC hub" from the format menu:

Press SUBMIT and accepted tracks will be loaded.

Both hub file and trackDb file can be submitted in this way. Also you can submit a UCSC hub via URL parameter:

http://epigenomegateway.wustl.edu/browser/?genome=hg18&datahub_ucsc=http://smithlab.usc.edu/trackdata/methylation/hub.txt

v29 (1 of 4): access HTTPS resources, including Dropbox

From version 29 you can now access tracks hosted on a HTTPS web server, including those that are publicly shared on the Dropbox.

Submitting an HTTPS track for display is identical as that with an HTTP track:

• submit from custom track panel at "CustomTK" > "Add new custom track"
• submit by datahub
• submit by URL parameter (same parameter names apply for HTTP and HTTPS tracks)
• submit by embedded browser

Try this example: a BAM track from Dropbox

http://epigenomegateway.wustl.edu/browser/?genome=hg19&custombam=dropbox+bam+track,https://dl.dropboxusercontent.com/u/6959481/hg19_test.bam,full

(this BAM track is for testing only and contains just tiny amount of data)




To host a track on Dropbox


You must have the Public folder in your dropbox. But for accounts created after Oct. 2012, you won't have it automatically. You need to create one yourself by following this link: https://www.dropbox.com/help/16/en

• upload your track files to the Public folder (so that they are publicly shared)
• for tabix and BAM files, put the index file in the same folder as track file
• obtain URL link to your track file by right clicking on the file and select "Copy public link"
• don't do this on the index file
• use this URL for track submission

Be aware not to make excessive use of Dropbox-hosted files.

Get the source code (and here) and refer to the new installation instructions.

v28 (2 of 2): track configuration

We've improved the track configuration options to fix bugs and bring more consistent behavior of the browser interface. There's some slight changes to the options shown as below, but now the functions should work more as expected than before.

Following is the configuration options on a quantitative track. You can get a similar looking panel for a feature-density track (e.g. a BAM track in density mode) without the "negative value" color option:

By checking the box for "apply to all tracks", your next configuring action will be applied to all the tracks in the browser (it used to be just those tracks in genome heatmap), well, for all applicable ones. Such that the gene track color won't be changed along if you change the positive value color for quantitative tracks.

Following is configuration options for an long range interaction track:

If you are configuring a long range interaction track in "heatmap" mode, the "height" option will appear. And if the track is in "full" mode, the text options (font size, color etc.) will appear.

Finally, when you have the secondary panel in the browser, any configuration options applied on a track in the secondary panel will be automatically applied to the same track in the main panel.

v28 (1 of 2): multiple track selection

From version 28 it is possible to select multiple tracks using SHIFT-click and operate on the selected tracks as a batch.

Very simply, click on a track while pressing Shift key on your keyboard. The track name background will turn yellow:

Click again on a highlighted track will de-select it. To operate on selected tracks, right click on any one of them and see menu options. You can configure their rendering style (e.g. color and height), or drop them all together.

To cancel the selection, use the "cancel multiple select" option or simply right click on an un-selected track. The yellow highlight color will go away to indicate the cancellation.

You can still drag and vertically reorder a track while it's selected. But you can't move all of them together.

This feature has been tested to work on all major platforms including Windows, Mac, and Linux. Supported web browsers include IE10, Firefox, Google Chrome, Chromium, Safari.

Get the source code of this version from our website or dropbox.

v27 (3 of 3): custom track listing

We brought back a missing feature, which allows you to view the entire list of custom tracks that have been loaded.

Click "CustomTK" button and find the "List of all" option. You need to load a datahub or some custom tracks first or these options won't show up:

Click this option to see a listing of all your custom tracks:

Those ones that are already on display are shown as inactive labels. Click the active ones and select a bunch to display on the browser.

Such track listing function is necessary as it allows you to find tracks that are NOT ANNOTATED by any metadata terms.

Those annotated by metadata terms will show up in the facet table, as described in this post: v24 (3 of 3): facet panel

v27 (2 of 3): make screenshot for Genome snapshot

The Genome snapshot (used to be call "bird's eye view") is often found useful. It is now made more useful with the SVG output.

Simply click the "screenshot" button on top of the panel to do it. A few seconds later a link will appear right next to the button showing you the SVG file.

v27 (1 of 3): GENCODE V17 track for the human genome

GENCODE version 17 of the human genes are now on hg19. Credit goes to UCSC Genome Browser where the data was obtained. GENCODE is one of the most finely curated gene tracks out there, and we're really happy to have it in our Browser.

http://epigenomegateway.wustl.edu/browser/?genome=hg19&gftk=gencodeV17,full

Genes are assigned into 5 categories, distinguished by color:

      coding genes
      non-coding genes
      pseudogenes
      with problem!
      polyA signal

For the "problem" ones, their causes can be seen in the tooltip bubble, such as "retained_intron".

In the tooltip, links are given to the gene model's record in GENCODE database.



This is the start of the effort to improve all the gene tracks on our Browser, including the underlying mechanism. Right now the GENCODE V17 track is new format and is supported by new mechanism, alongside the old gene tracks such as refGene, GENCODE V11.

With the new mechanism we can reduce the dependence on mysql storage and store all the data in the compressed track file, so that the new gene tracks can work as custom tracks. On such basis a new track type is been developed to support the RNA-seq experiments.

v26 (3 of 3): smoothing curves

A minor improvement has been made that allows you to smooth the graph of a quantitative track using window mean values.

An un-smoothed numerical track might look like this:

To smooth the track, right click on the track graph and choose "Configure". Check the "Apply smoothing window" checkbox, and adjust window size:

The graph updates after applying the 9-pixel smoothing window to the red track:

v26 (2 of 3): RepeatMasker tracks

A minor update to RepeatMasker tracks has been made, which is the ability to grade repetitive elements by their Smith-Waterman alignment scores.

The updated RepeatMasker tracks are available for following genomes: hg18, hg19, mm9, mm10, rn4, danRer7, dm3. All the RepeatMasker track data were downloaded from UCSC Genome Browser.

Go to browser and show human hg19 genome. At Tracks > Genomic annotation tracks > RepeatMasker, you can see a long list of tracks. Each track is one "class" of repeats, click the arrow following the track to see tracks of families from this class:

Click track L1 (LINE) to display it, which is the "L1" family from "LINE" class:

The L1 elements in above screenshot show various shades of color, which are determined by the greatest SW score of all L1 elements in the view range. Click on an element to see details:

Right click on the L1 track and choose "Configure". You can find options about what kind of scores can be used to grade the elements, or you can choose to disable the score and all items will become fully visible:

v26 (1 of 3): SNP track

Please join us on Google+ for discussions!

SNP information is a long-desired feature and we've finally got it on our browser. Credit goes to UCSC Genome Browser for making SNP information nicely curated and easily accessible.

In version 26 only the human hg19 genome has its SNP track (dbSNP release 137). We are working to add SNP tracks for all applicable genomes as well as enabling SNP custom tracks.

Click to see the SNP track.

Display hg19 SNP track

Go to the browser website and display human hg19 genome. Click "Tracks" > "Genomic annotation tracks", and find SNP track in "Variation" category:

Click the SNP track item to show the track on the browser:

By default the SNP track is shown in "full" mode, with the "rs..." name printed on the left of SNP location. SNPs are colored differently according to their classification:

•       single nucleotide variation
•       insertion/deletion
•       heterozygous variation
•       microsatellite
•       text name but not sequence
•       a cluster of multiple classes
•       multiple nucleotide polymorphism
•       insertion
•       deletion

Click on a SNP to see details about it:

Erratum: rs78276647 should be on "forward" strand

You can use the "link" on the top-right of the tooltip to see original record of this SNP in dbSNP website.

Search for SNPs

To search for SNPs, you need to have SNP track displayed first.

Right click on SNP track and find the search box:

Enter SNP name in the box and press Enter to find the hit:

Click the hit to show it in browser. The hit SNP will be highlighted:

Get v26 source code here, or here.

v25: new display methods for methylC-seq and RRBS experiments

Version 25 features a nice way to display CpG methylation data, and the track background color configuration.

CpG methylation track

Tracks like those generated by methylC-seq (bisulfite sequencing), and Reduced Representation Bisulfite sequencing (RRBS) assays are single-base resolution. There won't be any data unless there's a CpG site. Traditionally such tracks are displayed as numerical track with a number ranging from 0-1 for all bases. That leads to a confusion of "0 value (no methylation)" and "lack of data (not a CpG)".

Now a new display method is available to address this issue:

Click here to see this example

This example shows two methylC-seq tracks in human hg19. Methylation levels over CpG sites are marked out by red/blue bars, and the "counter-value" is marked out with gray. A long gray bar means the CpG site has very low methylation level. This way you can tell a unmethylated CpG site from those blank regions with no CpG sites.

This rendering method is suitable for numerical data with incomplete coverage of the entire genome. In the other words, if your track hasn't got a value for every bp in the genome, you should use this display method.

To use this display method, convert your track into bedGraph format.

To turn on the effect, add this attribute in the track object in the datahub:

barplot_bg:"#cccccc",

Or in the embedding code, add this:

barplotbackground:"#cccccc",

Track background

Now it's possible to apply background color to tracks. Simply check the "use background color" option in Configure menu:

To apply background color in datahub or embedded browser, add this in track object:

backgroundcolor:"#cccccc",

v24 (3 of 3): facet panel

"Facet panel" is a meaningful way to present large track set using metadata annotation. Version 24 features much improved facet table function.

• Improved user interface design
• Unified support on both native and custom metadata vocabularies

  Find the facet panel  

At the browser, click "Tracks" > "Experimental assay tracks". Following panel will be shown (example from hg19):

To change row definitions (principle facets), click "Sample" on the header to see available choices:

The facet panel can be configured into a tree by using only the Row option:

  Facet panel for custom metadata  

First, load a datahub. You can click following link to load a public hub in hg18 genome:

http://epigenomegateway.wustl.edu/browser/?genome=hg18&publichub=mm1s

Then open the facet panel:

Now you can see two facet tables. The table on top in colored border is from the public hub (named Multiple Myeloma Data Gateway).  The table on the bottom is the original native metadata vocabulary. The two tables are organized by two separate metadata vocabularies, but can be used in the same way.

  Using metadata colormap  

Both native and custom metadata terms can be chosen for display in metadata color map. Right click on the terms and choose "Add" option:

The metadata vocabulary tree will be shown. Check the checkbox for a term to add this term to color map. If a custom vocabulary has been loaded, it will also be shown as a tree with shaded background, along with the native tree:

v24 (2 of 3): JSON datahub format

Last modified: April 16, 2014

Please refer to the Datahub page on Wubrowse Wiki. This post is no longer updated.

From version 24 the Browser supports JSON datahub. We still maintain the support of tabular text hub format, but it is deprecated and we will drop the support in future.

JSON format is so much better, both for users and developers. Take a look at this feature-rich example datahub:

http://vizhub.wustl.edu/hubSample/hg19/hub.json

  Defining a track  

A track is defined as an object:

{
    type:"bedgraph",
    url:"http://vizhub.wustl.edu/hubSample/hg19/qual3.gz",
    name:"a track with quantitative values",
    mode:"show",
    custom_annotation:["aa","cc"],
    colorpositive:"#ff3333/#b30000",
    height:40,
    fixedscale:{min:0, max:10},
},

• type
• Required
• Track type. Value is bedGraph/bed/bigWig/categorical/BAM/longrange. 
• Names are case insensitive.
• url
• Required
• URL of the track file
• name
• Label to be displayed along with the track. Not an unique identifier.
• mode
• Display mode of the track. If the track will be displayed by default, use show/full/thin/density according to its track type. Use "hide" so the track will be hidden by default.
• If this attribute is not provided, the track will be hidden by default.
• custom_annotation
• Annotation by custom metadata vocabulary. The vocabulary must be defined in the same hub. Value is list of attributes.
• annotation
• Annotation by native metadata terms, must use term ID. For internal use.
• colorpositive
• Rendering color for positive numerical values
• Optionally a second color can be supplied following a slash, this color is for values beyond max threshold. Numerical track only.
• colornegative
• Same as colorpositive but for negative values
• fixedscale
• Fixed Y scale threshold values
• height
• Plot height for numerical and categorical tracks
• details
• Itemized details in the form of key:value pairs. Can be displayed by menu option. 
• Example value: {'antibody':'CTCF','protocol':'standard chip-seq',}
• details_text
• Same as details but is a long string. Mainly for internal use and details is preferred. 
• Example: "antibody=CTCF; protocol=standard chip-seq; "
• geo
• Astring of GEO accessions
• Example: "GSM123,GSM456"
• categories
• Category information for categorical tracks. 
• Value is {id:["name","color"],id2:["name2","color2"], ...}

Following are experimental attributes:

• group: to place tracks inside a group, value is integer 1/2/3... Numerical tracks in the same group  share the same Y scale range, and the Y scale is automatically determined to be extreme values of all tracks in the group. You thus cannot change Y scale type to threshold-based for member tracks.
• normalize:
• total_mapped_reads: 

  Defining a metadata vocabulary  

The metadata vocabulary can be as complex as needed:

• Hierarchical in nature. Arbitrary depth
• Tree or directed acyclic graph is supported, but not cycles
• 
  

{
type:"metadata",
vocabulary:{
    "epigenetic mark":{
        "DNA methylation":["aa","bb","cc"],
        "histone mark":["dd","ee"],
        },
    "rna-seq":{
        "mRNA":["aa","ee"],
        "small RNA":["dd","bb"],
        },
     },
show:["epigenetic mark","rna-seq"],
tag:"My Metadata",
},

About the keywords:

• vocabulary: value is the actual metadata vocabulary. In this example, "epigenetic mark" is a root-level term. It has "DNA methylation" and "histone mark" as its children. "aa" is one of leaf-level attributes. Only leaf-level attributes can be used to annotate tracks
• show: the list of terms that will be shown in metadata colormap. Both leaf or non-leaf terms can be used
• tag: optional name of this vocabulary

Please note that you can only define one vocabulary in a hub.

  Making gene sets  

  Adding terms from native metadata vocabulary   

{
type:"native_metadata_terms",
list:["Assay","Sample",30002],
},

"list" contains native metadata term names or ID, and they will show up in the metadata color map on loading the hub.

  Comments  

Any lines starting with '#' will be treated as comment and will not be parsed.

A comment must takes full lines, but not following any JSON statements, or have space characters proceeding it.

'#' comment is a feature designed to help users maintain their hub files. Technically the '#' comment is not legitimate JSON syntax, and thus should be avoided if your hub file will be handled by any third-party software.

  Using JSON hubs  

To submit a track hub on the browser, click "CustomTK" > "+ Add new custom tracks" > "DataHub", enter the hub file URL and click submit.

(You need to toggle the selection box to "json" to submit a JSON hub)

The hub can also be displayed via the "datahub_jsonfile" parameter in URL:

http://epigenomegateway.wustl.edu/browser/?genome=hg19&datahub_jsonfile=http://vizhub.wustl.edu/hubSample/hg19/hub.json

v24 (1 of 3): new genomes

From version 24 (download, or here), reference genomes of many new species are available on our Browser:

* Soybean Glycine max, version 189

* Common bean Phaseolus vulgaris, version 218

* Chinese cabbage Brassica rapa, version 1.1

* Autographa californica nucleopolyhedrovirus (no version info)

Go to the browser and see all available genomes.
The genomes are now grouped by Kingdom. Residents from Animalia are shown below:

Click Plantae and you will find out a list of edibles:

If you would like to publish your data from these genomes, or have additional genomes added, please contact us!

v23: custom categorical track

The categorical track represents categorical information along the chromosome sequence. Typical example is Chromatin State (chromhmm), as shown in following example:

Now you can display your own track data in the form of custom categorical track, for instance you might show various types of SNPs in different colors.

To prepare categorical track, convert your data into a text file with 4 columns in each row. The columns are:

1. chromosome name
2. feature start coordinate
3. feature stop coordinate
4. category ID

Category ID is positive integers starting from 1. Each integer corresponds to a category and will be rendered using its own color.

Compress and index this text file:

$ bgzip myfile.txt
you got "myfile.txt.gz"

$ tabix -p bed myfile.txt.gz
you got "myfile.txt.gz.tbi"

Put both "myfile.txt.gz" and "myfile.txt.gz.tbi" on the same directory of a web server.

Go to the browser, click "CustomTK" and then "Add new tracks", from the list of custom track types, push the button labeled "Categorical data":

You will see the track submission interface:

Enter URL to the file "myfile.txt.gz" or something, and name this track.

Also specify how many categories are there in your file. From the list of text boxes, enter name of each category, and choose a color.

Then click Submit to show this track on the browser.

Once displayed, you can right click on your categorical track and see the list of categories, or change color setting.

The custom categorical track can be saved and restored as session.


Version 23 source code is available from:
http://epigenomegateway.wustl.edu/info/source/
https://dl.dropboxusercontent.com/u/6959481/subtleKnife.v23.tgz

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.