sites that use the USCS browser

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Steve Fischer

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Aug 22, 2014, 7:17:07 PM8/22/14
to gen...@soe.ucsc.edu
Hi,

We are evaluating a number of genome browser systems, such as UCSC Browser, JBrowse and GenomeViewer for use as the Genome Browser on the EuPathDB websites.  These sites are databases that hold genome information for parasites.

As part of our evaluation we like to look at sites, besides the main UCSC Browser and mirrors, that use this software.  I am having trouble finding examples.   Can you refer me to any?

Thanks,
Steve

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Robert Kuhn

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Aug 22, 2014, 7:35:26 PM8/22/14
to Steve Fischer, UCSC Genome Browser Mailing List
Hi, Steve,

You probably want to post this to the genome-mirror mailing list.
Then people who are mirroring the Browser are likely to see it and
can contact you with their URLs.

Or you could look in the genome-mirror list archives:

https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror

Alternatively, you should consider using the Assembly Hubs mechansim,
which allows users to put their genomes on our public instance of the
Browser without downloading or installing the code locally.  In that case,
you simply host the relevant files to make your own assembly.

The following link:

http://genome.ucsc.edu/cgi-bin/hgHubConnect

goes to a page with a further link to the User's Guide as well as offering
several remotely-hosted non-UCSC genome assemblies, such as Arabidopsis.
and Drosophila simulans for you to look at.

regards,

      --b0b kuhn
    ucsc genome bioinformatics group
 


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Steve Fischer

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Aug 25, 2014, 12:08:54 PM8/25/14
to Robert Kuhn, UCSC Genome Browser Mailing List
Hi Robert,

Thanks for the response.

We want to host our own completely independent installation of the browser, with our own data, integrated into our websites (eg PlasmoDB.org).  Currently we use GBrowse for this but want to evaluate other browsers.   We don't want to mirror.

I looked at the Hub Connect pages like you suggested, but didn't find any links to sites that are hosting their own independent genome browser.

Any further ideas or leads?

Thanks,
Steve
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