[Gmod-help] Re: DIYA / DIYG

[Dave Clements]

Hi Andrew,

Thanks for the update on DIYA and DIYG.  I'm pretty well convinced that
Galaxy is on it's way to total worldwide domination.  The Galaxy group has a
human/vertebrate emphasis historically, so prokaryote functionality would be
a great addition.

However, I don't (yet) see Galaxy as a DIYA replacement.  Until Galaxy has
APIs for programmatically using it, I think DIYA still meets a separate
need.

GMOD has an on-off relationship with virtual appliances.  We certainly think
they are a grand idea and use them in our courses, but I don't think we have
ever produced a production ready system.  We do currently have a grant
proposal to cloud-enable GMOD components like GBrowse and JBrowse.  Please
send an e-mail to help at gmod.org, if and when it looks like you may start
down this path.

Good to hear from you,

Dave C


On Fri, May 21, 2010 at 5:56 AM, andrew stewart
<andrew.c.stewart at gmail.com>wrote:

> Hey Dave,
>
> That sounds great. Let me know if you need me to do anything.
>
> I apologize for the news being slow on the DIYA front, I switched jobs back
> in January and am not really in the microbial annotation business anymore.
>
> However, I have some good news!  I was attending the Galaxy Developers
> Conference this past weekend at CSH, and mused about ditching the pipeline
> aspect of DIYA and turning its individual components into a set of Galaxy
> tools (James Taylor was very supportive of this idea, mentioning that there
> is a lack of annotation tools in Galaxy).  So that's the direction I see
> DIYA going in the future.
>
> Do It Yourself Genomics (DIYG, the sourceforge project that DIYA falls
> under) I would like to see finally develop into a Virtual Appliance for
> distribution that bundles DIYA with Galaxy, GBrowse, etc, providing
> researchers a very easy-to-deploy solution to take their NGS data from raw
> sequence all the way to a fully annotated GMOD sequence database instance.
> (Probably also offer a 'worker node' image for deployment across a cluster
> or in something like Amazon's EC2)
>
> I know there have been some GMOD virtual machine projects in the past.  I'd
> be very interested in synching up with anyone who still maintains an active
> interest in this area.
>
>
> cheers,
> Andrew
>
>
> On Thu, May 20, 2010 at 11:46 PM, Dave Clements <clements at nescent.org>wrote:
>
>> Hi Andrew,
>>
>> The mailing list search function at SourceForge is notoriously
>> frustrating.  To hopefully address this I'm setting up an archive of GMOD
>> mailing lists at Nabble.com.  See
>>
>>
>> http://gmod-generic-model-organism-database-project.827538.n3.nabble.com/
>>
>> Would you like the DIYA mailing lists to be archived at Nabble?  I can set
>> this us as a GMOD subproject.  Or, you could set it up as a separate DIYG
>> project at Nabble.  Either way, we would link to it from the GMOD web site.
>>
>> After I'm done getting Nabble setup, I'll do the same thing at Gmane.org.
>> I'll assume that anything I do (or don't do) for DIYA at Nabble, I'll also
>> do (or don't do) at Gmane as well.
>>
>> Dave C.
>>
>> --
>> http://gmod.org/wiki/GMOD_News
>> http://gmod.org/wiki/Calendar
>> http://gmod.org/wiki/Help_Desk_Feedback
>>
>
>


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