Custom storage for GBrowse

> Hi everyone,
>
>
>
> I want to try writing my own data structure/storage for GBrowse tracks
> instead of using database such as MySQL.
>
> Can anyone tell me which interfaces to implement, i.e. which parts of
> GBrowse I have to extend or use as reference?
>
> Is there any resources I can read regarding this subject? Thanks!
>
>
>
> Regards,
>
> Fabianus
>
>
>
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>

> Hi everyone,
>
>
>
> I want to try writing my own data structure/storage for GBrowse tracks
> instead of using database such as MySQL.
>
> Can anyone tell me which interfaces to implement, i.e. which parts of
> GBrowse I have to extend or use as reference?
>
> Is there any resources I can read regarding this subject? Thanks!
>
>
>
> Regards,
>
> Fabianus
>
>
>
>

> Hi Scott,
>
> Thanks for the reply. After reading the modules you mentioned, I  
> realize
> that I may not need to write my own adaptor after all.
>
> What I want to try is a new way of storing dense data track. For this
> purpose, I just need to write another version of  
> Bio::Graphics::Wiggle,
> and perhaps wiggle_xyplot as well. Is this correct?
>
> Regards,
> Fabi
>
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>
> -----Original Message-----
> From: Scott Cain [mailto:scott@...]
> Sent: Wednesday, October 07, 2009 9:13 PM
> To: Fabianus Hendriyan MULAWADI
> Cc: gmod-gbrowse@...
> Subject: Re: [Gmod-gbrowse] Custom storage for GBrowse
>
> Hello Fabianus,
>
> Generally, this is a non-trivial undertaking, and the resulting data
> adaptor will not perform as well as one specifically designed for
> GBrowse, like the ones for Bio::DB::GFF or Bio::DB::SeqFeature::Store.
> So I generally try to suggest in cases like this that your time would
> probably be better spent writing a robust GFF3 dumper for your
> database.  That way, you can dump out your data into GFF3 as often as
> you need to in order to create a SeqFeature::Store database from the
> data (which is the one I would suggest you use).
>
> If you don't want to do that for whatever reason, there is in fact no
> documentation for writing a data adaptor.  If you implement the
> Bio::DasI interface it should work, and there are examples of data
> adaptors written specifically for Chado, BioSQL and Samtools in the
> gmod svn repository:
>
>  http://gmod.svn.sourceforge.net/viewvc/gmod/gbrowse-adaptors/trunk/
>
> and these could serve as examples.
>
> Scott
>
>
> On Wed, Oct 7, 2009 at 5:00 AM, Fabianus Hendriyan MULAWADI
> <mulawadifh@...> wrote:
>> Hi everyone,
>>
>>
>>
>> I want to try writing my own data structure/storage for GBrowse  
>> tracks
>> instead of using database such as MySQL.
>>
>> Can anyone tell me which interfaces to implement, i.e. which parts of
>> GBrowse I have to extend or use as reference?
>>
>> Is there any resources I can read regarding this subject? Thanks!
>>
>>
>>
>> Regards,
>>
>> Fabianus
>>
>>
>>
>>
> ------------------------------------------------------------------------
> ------
>> Come build with us! The BlackBerry(R) Developer Conference in SF, CA
>> is the only developer event you need to attend this year. Jumpstart
> your
>> developing skills, take BlackBerry mobile applications to market and
> stay
>> ahead of the curve. Join us from November 9 - 12, 2009. Register now!
>> http://p.sf.net/sfu/devconference
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse@...
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research