[Gmod-ajax] script to generate genome images

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[Gmod-ajax] script to generate genome images

Parul Kudtarkar
Hi,

Are there any scripts to generate genomes images, something analogous to
gbrowse's gbrowse_img?
http://gmod.org/wiki/GBrowse_img

Thanks and regards,
Parul Kudtarkar

--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org


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Re: script to generate genome images

Robert Buels-2
No, JBrowse doesn't have anything like this currently.

Most of the time, people just embed a running JBrowse in the place where
they would have used a gbrowse_img.  See
http://gmod.org/wiki/JBrowse_Configuration_Guide#Embedded_mode.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 10/18/2013 02:19 PM, Parul Kudtarkar wrote:

> Hi,
>
> Are there any scripts to generate genomes images, something analogous to
> gbrowse's gbrowse_img?
> http://gmod.org/wiki/GBrowse_img
>
> Thanks and regards,
> Parul Kudtarkar
>
> --
> Scientific Programmer
> Center for Computational Regulatory Genomics
> Beckman Institute,
> California Institute of Technology
> http://www.spbase.org
>
>
> ------------------------------------------------------------------------------
> October Webinars: Code for Performance
> Free Intel webinars can help you accelerate application performance.
> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from
> the latest Intel processors and coprocessors. See abstracts and register >
> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
>

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Re: script to generate genome images

Parul Kudtarkar
Thanks Rob, That should work for us as well.

Thanks and regards,
Parul Kudtarkar

> No, JBrowse doesn't have anything like this currently.
>
> Most of the time, people just embed a running JBrowse in the place where
> they would have used a gbrowse_img.  See
> http://gmod.org/wiki/JBrowse_Configuration_Guide#Embedded_mode.
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 10/18/2013 02:19 PM, Parul Kudtarkar wrote:
>> Hi,
>>
>> Are there any scripts to generate genomes images, something analogous to
>> gbrowse's gbrowse_img?
>> http://gmod.org/wiki/GBrowse_img
>>
>> Thanks and regards,
>> Parul Kudtarkar
>>
>> --
>> Scientific Programmer
>> Center for Computational Regulatory Genomics
>> Beckman Institute,
>> California Institute of Technology
>> http://www.spbase.org
>>
>>
>> ------------------------------------------------------------------------------
>> October Webinars: Code for Performance
>> Free Intel webinars can help you accelerate application performance.
>> Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most
>> from
>> the latest Intel processors and coprocessors. See abstracts and register
>> >
>> http://pubads.g.doubleclick.net/gampad/clk?id=60135031&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>>
>


--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org


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Re: script to generate genome images

Keiran Raine
In reply to this post by Robert Buels-2
Hi Robert,

With regards to this, many of our scientific staff like the ability to be ably to do this for several reasons:

1. Run a script to get all regions around variants of interest (#345 will address this to some degree).
2. Inclusion in posters, presentations and papers.

(2) can be addressed by adding the ability to save a view

For more general 'wget' type use similar to gbrows_img, a few of the developers in our group came up with an option provided 'save image' was available.  If this was available it should be possible to use a headless web-kit browser on a server to return the images.

Just some thoughts, not sure how feasible, although I've poked around and there does seem to be some examples for stitching together image tiles, e.g. TileStitchingPrinting.

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

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

On 19 Oct 2013, at 21:50, Robert Buels <[hidden email]> wrote:

No, JBrowse doesn't have anything like this currently.

Most of the time, people just embed a running JBrowse in the place where
they would have used a gbrowse_img.  See
http://gmod.org/wiki/JBrowse_Configuration_Guide#Embedded_mode.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 10/18/2013 02:19 PM, Parul Kudtarkar wrote:
Hi,

Are there any scripts to generate genomes images, something analogous to
gbrowse's gbrowse_img?
http://gmod.org/wiki/GBrowse_img

Thanks and regards,
Parul Kudtarkar

--
Scientific Programmer
Center for Computational Regulatory Genomics
Beckman Institute,
California Institute of Technology
http://www.spbase.org


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-- The Wellcome Trust Sanger Institute is operated by Genome Rese arch 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.

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