proposal to add RDF services to GBrowse

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proposal to add RDF services to GBrowse

ben.vvalk
Hi GBrowse developers,

I've been working on a project called SADI for GMOD, which is basically an RDF version of DAS: http://code.google.com/p/sadi/wiki/SADIforGMOD.
It is implemented as a set of Perl CGI scripts running over a Bio::DB::SeqFeature::Store (with support for Bio::DB::Das::Chado coming soon).

I was wondering if you would be open to bundling my services with GBrowse? I think it would be a really good fit.

If you are okay with the idea in principle, I will work out how to integrate it and send over a patch for your review.

Btw, I work in the Wilkinson lab at UBC, which has previously contributed some BioMoby services to GBrowse.  Thanks for your consideration!

-- Ben Vandervalk


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Re: proposal to add RDF services to GBrowse

Robert Buels
Hi Ben,

Ah, this is an interesting idea, serving SADI from a
Bio::DB::SeqFeature::Store.

After reading through it a bit, I have some thoughts:

There don't seem to be any automated tests for this code.  I haven't
delved into it in-depth, but the absence of automated tests raises a lot
of red flags for me regarding its long-term maintainability.  Have you
considered writing tests?

Also, if you're still developing this code, I'd also recommend that you
look into using Plack for interfacing with the web server instead of
bare CGI.  It gives users of the code a lot more options for how it can
be deployed, whether under regular CGI, mod_perl, fastcgi, or as a
standalone server.  Using it can also make the code easier to test.

What do you think?

Rob


On 08/08/2011 10:53 AM, Ben Vandervalk wrote:

> Hi GBrowse developers,
>
> I've been working on a project called SADI for GMOD, which is basically
> an RDF version of DAS: http://code.google.com/p/sadi/wiki/SADIforGMOD.
> It is implemented as a set of Perl CGI scripts running over a
> Bio::DB::SeqFeature::Store (with support for Bio::DB::Das::Chado coming
> soon).
>
> I was wondering if you would be open to bundling my services with
> GBrowse? I think it would be a really good fit.
>
> If you are okay with the idea in principle, I will work out how to
> integrate it and send over a patch for your review.
>
> Btw, I work in the Wilkinson lab at UBC, which has previously
> contributed some BioMoby services to GBrowse.  Thanks for your
> consideration!
>
> -- Ben Vandervalk
>
>
>
> ------------------------------------------------------------------------------
> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
> The must-attend event for mobile developers. Connect with experts.
> Get tools for creating Super Apps. See the latest technologies.
> Sessions, hands-on labs, demos&  much more. Register early&  save!
> http://p.sf.net/sfu/rim-blackberry-1
>
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse


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Re: proposal to add RDF services to GBrowse

ben.vvalk


On Wed, Aug 10, 2011 at 3:38 PM, Robert Buels <[hidden email]> wrote:
Hi Ben,

Ah, this is an interesting idea, serving SADI from a Bio::DB::SeqFeature::Store.

After reading through it a bit, I have some thoughts:

There don't seem to be any automated tests for this code.  I haven't delved into it in-depth, but the absence of automated tests raises a lot of red flags for me regarding its long-term maintainability.  Have you considered writing tests?

Also, if you're still developing this code, I'd also recommend that you look into using Plack for interfacing with the web server instead of bare CGI.  It gives users of the code a lot more options for how it can be deployed, whether under regular CGI, mod_perl, fastcgi, or as a standalone server.  Using it can also make the code easier to test.

What do you think?

Rob


Hi Rob,

Thanks very much for taking the time to look at my software (and sorry for the slow reply!).

I absolutely understand about the unit tests and I will be writing some soon.

I didn't know about Plack and I didn't understand it at first; but now that I do, I don't see any downsides to using it. As you say, it will make life easier both for my users (setup-wise) and for myself (testing-wise).  So thanks for the tip!

I'll get back to you when I've made those improvements.  It will probably be a few weeks (at least) since I am working on other stuff at the moment.

Later!

-- Ben

 


On 08/08/2011 10:53 AM, Ben Vandervalk wrote:
Hi GBrowse developers,

I've been working on a project called SADI for GMOD, which is basically
an RDF version of DAS: http://code.google.com/p/sadi/wiki/SADIforGMOD.
It is implemented as a set of Perl CGI scripts running over a
Bio::DB::SeqFeature::Store (with support for Bio::DB::Das::Chado coming
soon).

I was wondering if you would be open to bundling my services with
GBrowse? I think it would be a really good fit.

If you are okay with the idea in principle, I will work out how to
integrate it and send over a patch for your review.

Btw, I work in the Wilkinson lab at UBC, which has previously
contributed some BioMoby services to GBrowse.  Thanks for your
consideration!

-- Ben Vandervalk



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