Re: [Gmod-help] nominate SADI for GMOD as a new GMOD component

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Re: [Gmod-help] nominate SADI for GMOD as a new GMOD component

Hilmar Lapp
Can I +1 this in Google+ ?

-hilmar

On Jul 17, 2011, at 3:02 AM, Ben Vandervalk wrote:

Hi GMOD help,

I have just released the initial version of "SADI for GMOD", and I would like to nominate it as an official GMOD component. SADI for GMOD is a set of Perl CGI scripts which provide an RDF view of a Bio::DB::SeqFeature::Store database.  A basic description of the project is here:

         http://code.google.com/p/sadi/wiki/SADIforGMOD

I would love to put this information on the GMOD wiki, as that would greatly increase the project's visibilty.

I am employed to work on SADI for the next year or so, so I am in a very good position to provide support and further development for SADI for GMOD.  Also, I am game to continue supporting the project in the longer term as well.

Thanks for your consideration!

-- Ben Vandervalk

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================




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Re: [Gmod-help] nominate SADI for GMOD as a new GMOD component

Scott Cain
Hi Ben,

I think there is a future for SADI in GMOD.  If you haven't already,
please take a look at:

  http://gmod.org/wiki/GMOD_Membership#Software

Ideally, I'd like to see SADI talking to Chado rather than
SeqFeature::Store (or actually, in addition to, as there is no need to
do away with SFS connectivity), since when you are limited to SFS, you
are limiting the amount of information you can get to sequence
annotations, while a Chado database could provide so much more, like
genotypes, phenotypes, and natural diversity data (and stocks,
publications, controlled vocabularies...)

I suggested at BOSC that you consider trying Bio::DB::Das::Chado for
SADI, and I still think that is a good idea, though that solution
still suffers from the same limitation that connecting to a SFS
database does, namely that it would be limited to sequence
annotations.  However, I would hope that this would just be a first
step, and as more functionality for accessing different data types
could evolve from there.

How does that sound?

Scott


On Sat, Jul 16, 2011 at 9:02 PM, Ben Vandervalk <[hidden email]> wrote:

> Hi GMOD help,
>
> I have just released the initial version of "SADI for GMOD", and I would
> like to nominate it as an official GMOD component. SADI for GMOD is a set of
> Perl CGI scripts which provide an RDF view of a Bio::DB::SeqFeature::Store
> database.  A basic description of the project is here:
>
>          http://code.google.com/p/sadi/wiki/SADIforGMOD
>
> I would love to put this information on the GMOD wiki, as that would greatly
> increase the project's visibilty.
>
> I am employed to work on SADI for the next year or so, so I am in a very
> good position to provide support and further development for SADI for GMOD.
> Also, I am game to continue supporting the project in the longer term as
> well.
>
> Thanks for your consideration!
>
> -- Ben Vandervalk
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Ries, the creator of the Lean Startup Methodology on "Lean Startup
Secrets Revealed." This video shows you how to validate your ideas,
optimize your ideas and identify your business strategy.
http://p.sf.net/sfu/appsumosfdev2dev
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Re: [Gmod-help] nominate SADI for GMOD as a new GMOD component

Siddhartha Basu
Excellent idea.
+1 from me on that.

-siddhartha

On Mon, 18 Jul 2011, Scott Cain wrote:

> Hi Ben,
>
> I think there is a future for SADI in GMOD.  If you haven't already,
> please take a look at:
>
>   http://gmod.org/wiki/GMOD_Membership#Software
>
> Ideally, I'd like to see SADI talking to Chado rather than
> SeqFeature::Store (or actually, in addition to, as there is no need to
> do away with SFS connectivity), since when you are limited to SFS, you
> are limiting the amount of information you can get to sequence
> annotations, while a Chado database could provide so much more, like
> genotypes, phenotypes, and natural diversity data (and stocks,
> publications, controlled vocabularies...)
>
> I suggested at BOSC that you consider trying Bio::DB::Das::Chado for
> SADI, and I still think that is a good idea, though that solution
> still suffers from the same limitation that connecting to a SFS
> database does, namely that it would be limited to sequence
> annotations.  However, I would hope that this would just be a first
> step, and as more functionality for accessing different data types
> could evolve from there.
>
> How does that sound?
>
> Scott
>
>
> On Sat, Jul 16, 2011 at 9:02 PM, Ben Vandervalk <[hidden email]> wrote:
> > Hi GMOD help,
> >
> > I have just released the initial version of "SADI for GMOD", and I would
> > like to nominate it as an official GMOD component. SADI for GMOD is a set of
> > Perl CGI scripts which provide an RDF view of a Bio::DB::SeqFeature::Store
> > database.  A basic description of the project is here:
> >
> >          http://code.google.com/p/sadi/wiki/SADIforGMOD
> >
> > I would love to put this information on the GMOD wiki, as that would greatly
> > increase the project's visibilty.
> >
> > I am employed to work on SADI for the next year or so, so I am in a very
> > good position to provide support and further development for SADI for GMOD.
> > Also, I am game to continue supporting the project in the longer term as
> > well.
> >
> > Thanks for your consideration!
> >
> > -- Ben Vandervalk
> >
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Gmod-devel mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-devel

------------------------------------------------------------------------------
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Ries, the creator of the Lean Startup Methodology on "Lean Startup
Secrets Revealed." This video shows you how to validate your ideas,
optimize your ideas and identify your business strategy.
http://p.sf.net/sfu/appsumosfdev2dev
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Re: [Gmod-help] nominate SADI for GMOD as a new GMOD component

ben.vvalk
In reply to this post by Scott Cain
On Mon, Jul 18, 2011 at 5:41 PM, Scott Cain <[hidden email]> wrote:
Hi Ben,

I think there is a future for SADI in GMOD.  If you haven't already,
please take a look at:

 http://gmod.org/wiki/GMOD_Membership#Software

Ideally, I'd like to see SADI talking to Chado rather than
SeqFeature::Store (or actually, in addition to, as there is no need to
do away with SFS connectivity), since when you are limited to SFS, you
are limiting the amount of information you can get to sequence
annotations, while a Chado database could provide so much more, like
genotypes, phenotypes, and natural diversity data (and stocks,
publications, controlled vocabularies...)

I suggested at BOSC that you consider trying Bio::DB::Das::Chado for
SADI, and I still think that is a good idea, though that solution
still suffers from the same limitation that connecting to a SFS
database does, namely that it would be limited to sequence
annotations.  However, I would hope that this would just be a first
step, and as more functionality for accessing different data types
could evolve from there.

How does that sound?

Scott


Hi Scott,

No problem about adding Chado support. That shouldn't be a big deal and I would like to do it anyway.  Also, I am cool with the requirements on the GMOD members page.

Later!

-- Ben

  

On Sat, Jul 16, 2011 at 9:02 PM, Ben Vandervalk <[hidden email]> wrote:
> Hi GMOD help,
>
> I have just released the initial version of "SADI for GMOD", and I would
> like to nominate it as an official GMOD component. SADI for GMOD is a set of
> Perl CGI scripts which provide an RDF view of a Bio::DB::SeqFeature::Store
> database.  A basic description of the project is here:
>
>          http://code.google.com/p/sadi/wiki/SADIforGMOD
>
> I would love to put this information on the GMOD wiki, as that would greatly
> increase the project's visibilty.
>
> I am employed to work on SADI for the next year or so, so I am in a very
> good position to provide support and further development for SADI for GMOD.
> Also, I am game to continue supporting the project in the longer term as
> well.
>
> Thanks for your consideration!
>
> -- Ben Vandervalk
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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