[Gmod-ajax] JBrowse on UCSC?

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[Gmod-ajax] JBrowse on UCSC?

Raymond Wan-2
Hi all,

Sorry if this topic has been discussed before (I don't recall having
seen it...), but I was just reading the "State of the Browser" entry
on the JBrowse web site [1], and there has been something I've been
wondering about for a while...

Would anyone know if development / support on GBrowse officially stopped?

And, if so, are there plans for sites such as UCSC to start using
JBrowse?  (I'm not sure if anyone on this mailing list would know the
answer to this...)

I have asked users to try to get use to JBrowse, but the discussion
always leads back to "what UCSC is using".  (I'll admit that UCSC's
GBrowse is perhaps more appealing to them because of my lack of skill
in maximizing JBrowse's potential in terms of editing configuration
files...)

Thank you!

Ray

[1]  http://jbrowse.org/state-of-the-browser-2016/

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bring their own devices (BYOD) to work are irked by the imposition of MDM
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Re: JBrowse on UCSC?

Keiran Raine
Hi,

Are UCSC using GBrowse, do you mean internally?  The public site is there own browser, not GBrowse.

The biggest resistance to using JBrowse over GBrowse for us has always been image generation.  PhantomJS works but has limitations as there isn’t a definitive event to indicate all the tracks have completed rendering.

We actually have GBrowse, JBrowse and an IGV data server running.  Unfortunately what will decide our future direction is likely to be which tools support CRAM first.  Technically I suspect this is GBrowse as Bio::DB::Sam has been converted to Bio::DB::HTS but I don’t know of anyone attempting to set the adaptor to Bio::DB::HTS yet (I may try if I get some time).

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 11 May 2016, at 10:01, Raymond Wan <[hidden email]> wrote:

Hi all,

Sorry if this topic has been discussed before (I don't recall having
seen it...), but I was just reading the "State of the Browser" entry
on the JBrowse web site [1], and there has been something I've been
wondering about for a while...

Would anyone know if development / support on GBrowse officially stopped?

And, if so, are there plans for sites such as UCSC to start using
JBrowse?  (I'm not sure if anyone on this mailing list would know the
answer to this...)

I have asked users to try to get use to JBrowse, but the discussion
always leads back to "what UCSC is using".  (I'll admit that UCSC's
GBrowse is perhaps more appealing to them because of my lack of skill
in maximizing JBrowse's potential in terms of editing configuration
files...)

Thank you!

Ray

[1]  http://jbrowse.org/state-of-the-browser-2016/

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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Re: JBrowse on UCSC?

Serguei Simonov-2
In reply to this post by Raymond Wan-2
Interesting topic,

I like JBrowse more than any other (I tested dozens of different models). But my colleagues choose UCSC browser.

Try to explain the reasons as I know:

- UCSC more documented and they have a program for education.
- UCSC based on very old html technologies - so it works on any web browser (including IE). Minimum javascript. All the pictures are online generated .gif files which save in a big storage and delete periodically.
- UCSC browser has a support (table browser) for operation on whole genome.
- it’s fast (implement on C) and recompile every two weeks
- The most important - it accumulate and updated a lot of genetic data.

But as I understand they both developed in UC (sc and Berkelay).

May be other opinions?

Serguei

 

> On 11 May 2016, at 12:01, Raymond Wan <[hidden email]> wrote:
>
> Hi all,
>
> Sorry if this topic has been discussed before (I don't recall having
> seen it...), but I was just reading the "State of the Browser" entry
> on the JBrowse web site [1], and there has been something I've been
> wondering about for a while...
>
> Would anyone know if development / support on GBrowse officially stopped?
>
> And, if so, are there plans for sites such as UCSC to start using
> JBrowse?  (I'm not sure if anyone on this mailing list would know the
> answer to this...)
>
> I have asked users to try to get use to JBrowse, but the discussion
> always leads back to "what UCSC is using".  (I'll admit that UCSC's
> GBrowse is perhaps more appealing to them because of my lack of skill
> in maximizing JBrowse's potential in terms of editing configuration
> files...)
>
> Thank you!
>
> Ray
>
> [1]  http://jbrowse.org/state-of-the-browser-2016/
>
> ------------------------------------------------------------------------------
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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Re: JBrowse on UCSC?

Raymond Wan-2
In reply to this post by Keiran Raine
Hi Keiran,


On Wed, May 11, 2016 at 5:30 PM, Keiran Raine <[hidden email]> wrote:
> Are UCSC using GBrowse, do you mean internally?  The public site is there
> own browser, not GBrowse.


It isn't?  Oh...I never realised this!  I guess because UCSC and
GBrowse's default colour scheme looks similar, I thought UCSC was
using it?!?  (Much like Wikipedia uses the Mediawiki platform.)

Or maybe because they call it the "UCSC Genome Browser" and I somehow
thought it came from "GBrowse" (or vice-versa).

Thank you for clarifying!


> The biggest resistance to using JBrowse over GBrowse for us has always been
> image generation.  PhantomJS works but has limitations as there isn’t a
> definitive event to indicate all the tracks have completed rendering.
>
> We actually have GBrowse, JBrowse and an IGV data server running.
> Unfortunately what will decide our future direction is likely to be which
> tools support CRAM first.  Technically I suspect this is GBrowse as
> Bio::DB::Sam has been converted to Bio::DB::HTS but I don’t know of anyone
> attempting to set the adaptor to Bio::DB::HTS yet (I may try if I get some
> time).


We do use JBrowse, UCSC, and IGV, but from the perspective of IT
support, it is more efficient (i.e., easier for me :-) ) if there was
only one to worry about.

No doubt one will never be the best since each will have its own pros
and cons.  But you're right -- it's comes down to whichever one meets
the minimum requirements of "most" local users (since "all" is
impossible).

Thank you!

Ray

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
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