[Gmod-ajax] Ensembl data

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[Gmod-ajax] Ensembl data

James Morris
Hello,

I am developing a web application for GWAS results in specific  
phenotypes.

I would like to use JBrowse to allow users to explore the genomic  
region surrounding associations.

I plan to use the Ensembl database as the main source of data for the  
application.

I would therefore like to display the Ensembl human reference and some  
additional tracks like SNPs and genes in JBrowse.

Has somebody already done this and are files available? If this is not  
the case would it be difficult to do so or is there an easier solution  
such as using data from UCSC?

Many thanks,

James


--
 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.

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Re: Ensembl data

Suzanna Lewis-3
Gregg Helt has done most of the work needed to obtain UCSC data (we decided to do UCSC first and then Ensembl followed by Chado as third). He would have to  say where things stand at the moment, but I think it would be easier than starting from scratch.

-S
 
On Aug 4, 2010, at 3:39 AM, James Morris wrote:

> Hello,
>
> I am developing a web application for GWAS results in specific  
> phenotypes.
>
> I would like to use JBrowse to allow users to explore the genomic  
> region surrounding associations.
>
> I plan to use the Ensembl database as the main source of data for the  
> application.
>
> I would therefore like to display the Ensembl human reference and some  
> additional tracks like SNPs and genes in JBrowse.
>
> Has somebody already done this and are files available? If this is not  
> the case would it be difficult to do so or is there an easier solution  
> such as using data from UCSC?
>
> Many thanks,
>
> James
>
>
> --
> 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.
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>


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http://p.sf.net/sfu/dev2dev-palm
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Re: Ensembl data

Ian Holmes
Mitch has suggested that we prepackage the JSON files generated from
Ensembl and UCSC human annotation data (and possibly other common
datasets) for easy setup. This is in line with what we had planned to do
anyway, so we are going to go ahead and do this.

Suzanna Lewis wrote:

> Gregg Helt has done most of the work needed to obtain UCSC data (we decided to do UCSC first and then Ensembl followed by Chado as third). He would have to  say where things stand at the moment, but I think it would be easier than starting from scratch.
>
> -S
>  
> On Aug 4, 2010, at 3:39 AM, James Morris wrote:
>
>> Hello,
>>
>> I am developing a web application for GWAS results in specific  
>> phenotypes.
>>
>> I would like to use JBrowse to allow users to explore the genomic  
>> region surrounding associations.
>>
>> I plan to use the Ensembl database as the main source of data for the  
>> application.
>>
>> I would therefore like to display the Ensembl human reference and some  
>> additional tracks like SNPs and genes in JBrowse.
>>
>> Has somebody already done this and are files available? If this is not  
>> the case would it be difficult to do so or is there an easier solution  
>> such as using data from UCSC?
>>
>> Many thanks,
>>
>> James
>>
>>
>> --
>> 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.
>>
>> ------------------------------------------------------------------------------
>> The Palm PDK Hot Apps Program offers developers who use the
>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>> of $1 Million in cash or HP Products. Visit us here for more details:
>> http://p.sf.net/sfu/dev2dev-palm
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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