How To Integrate Mirror Ucsc Genome Browser Into Local Web Service

Question

[liqingyan]

I want to develop a web site with a function to show WIG data visually by using existing genome browser. for example: there is a page in my site, showing some database records, and I want to add some genome browser in this page to show WIG data visually.

1. UCSC genome browser is preferred, but how to integrate it to our web service.

2. Please recommend some other genome browser that can integrate easily.

Thanks for your help.

Answer 1

[Giovanni M Dall'Olio]

A solution that can be implemented in a short time and doesn't require too much maintenance is the UCSC Tracks Hubs.

Basically, you create your (big)Wig files and store them to a webserver. Then, people will be able to access to the tracks from any other UCSC browser installation (e.g. the one at UCSC), by adding a parameter to the URL. See this example of a UCSC Hub: http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://vizhub.wustl.edu/VizHub/RoadmapRelease3.txt

This solution is quick and easy, and you do not have to setup and configure a custom UCSC instance. Moreover, people will be able to use it from any other browser installation, and and compare it with their own datasets. However, I don't know exactly what you mean by "integrating the browser in your web service", and which type of web services you are developing, so I am not sure if this is useful for you.

P.s. even if you do not use track Hubs, have a look at the Track Hubs Database Definition document, which I think is the best documentation available for defining tracks in UCSC.

[Mary]

Yeah, I was also going to suggest this was the way to go. The hubs are a nice solution for exactly this issue.

Answer 2

[Sandeep]

I have never tried it myself but I came across this http://genomewiki.ucsc.edu/index.php/Main_Page.

There is detailed instructions to mirror UCSC browser.

Hope this helps