[Gmod-help] MOLGENIS

[Dave Clements]

Dear Morris,

I finished reading the "Beyond standardization" paper this morning.  I'm
very impressed with MOLGENIS and what the project is doing.  (I was also
impressed with XGAP when I read that paper).

MOLGENIS certainly aligns with GMOD's intent.  It is generic open-source
software that is widely applicable in biological research.  MOLGENIS takes
GMOD's "configurable and extensible" goal to new heights.  It also appears
to be a vibrant and growing project.  I'm guessing that the project would
have no problem meeting the "good faith commitment of support for at least 2
years"  requirement.

However, I can't yet see how MOLGENIS would address GMOD's interoperability
requirement, and that is a key requirement for us.  Interoperability is
usually achieved by either working with GFF files or Chado databases.  As
far as I can tell MOLGENIS does not work with either.  I did notice a paper
on using MOLGENIS with BioMart (haven't read it yet), but I don't think that
is enough.  BioMart works with any database schema out there, including ones
completely unrelated to biology.

Have you got any ideas on how MOLGENIS could meet the interoperability
requirement?

Thanks,

Dave C.

On Thu, May 13, 2010 at 4:29 PM, Dave Clements <clements at nescent.org> wrote:

> Dear Morris,
>
> I meant to give you a thoughtful response this week, but time has been hard
> to come by for the past several days.  (We just finished the 2010 GMOD
> Summer School and your email arrived while I was traveling.)
>
> The requirements for GMOD software are described on the
> http://gmod.org/wiki/GMOD_Membership page.  Can you take a look at those
> and let me know if you think MOLGENIS meets the requirements?  That page
> also describes the process of becoming part of GMOD.
>
> I'll take a closer look at MOLGENIS and then (hopefully!) give you a
> thoughtful response to this proposal.  If we still think we are a good match
> then we'll start the nominating process.
>
> I just read the XGAP paper last week (while flying to the summer school).
>
> I'm taking tomorrow (Friday) off.  I'll try to send you a response by the
> middle of next week.
>
> Thanks for your interest,
>
> Dave C.
>
>
>
>
> On Tue, May 11, 2010 at 7:43 AM, Morris Swertz <m.a.swertz at rug.nl> wrote:
>
>> Dear GMOD team,
>>
>> First, compliments on the great work with GMOD. Secondly I want to propose
>> adding our MOLGENIS project to the GMOD family. In particular because we now
>> embarked on animaldb, a project to manage experiments on model organisms, as
>> well as various genotype/phenotype efforts that overlap with GMOD
>> activities. Also we noticed GMOD expanding with the inclusion of affiliated
>> infrastructures like BioMART and Galaxy. We would like to make sure our
>> activities converge.
>>
>> Background: In the five-odd years we have developed a powerful database
>> generator software named MOLGENIS that generates web applications plus user,
>> R, Java, SOAP, REST, RDF and tab delimited exchange format. This formaly has
>> proven an excellent platform to rapidly prototype custom web applications
>> for life science experiments. With more and more users spread over the world
>> we would be delighted to make our work part of the GMOD network which we
>> think is a great way to make sure projects work together. Currently we are
>> about 10 developers as well as partners distributed over mainly Europe which
>> allows us to provide GMOD levels of support and help. We are preparing to
>> integrate into GMOD components and models so bind our communities together.
>> See attachement of our BOSC abstract for some more info.
>>
>> Hoping for a positive response we have proactively added some more
>> information to http://gmod.org/wiki/MolGenIS
>> Being a newcomer in GMOD not knowing ettiquette, thus we've not yet added
>> to the Database Tools section http://gmod.org/wiki/GMOD_Components
>>
>> Kind regards,
>> Morris Swertz
>>
>> http://www.molgenis.org
>> http://tinyurl.com/swertz-at-ebi
>> http://tinyurl.com/swertz-at-umcg
>>
>>
>>
>>
>
>
> --
> http://gmod.org/wiki/GMOD_News
> http://gmod.org/wiki/Calendar
> http://gmod.org/wiki/Help_Desk_Feedback
>



-- 
http://gmod.org/wiki/GMOD_News
http://gmod.org/wiki/Calendar
http://gmod.org/wiki/Help_Desk_Feedback
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20100525/73950a1c/attachment.html>