[GSoC] GSOC OBF & GMOD

Sun Mar 9 18:58:54 UTC 2014

I've added the WormBase idea to the OBF GSoC wiki page:
http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas#WormBase:_data_visualization

The "cross-project ideas" section of the page also now links to GMOD's
ideas page. Since the student application period is about to begin, I think
this gives students enough to chew on and can stay as it is.

On Wed, Mar 5, 2014 at 6:33 AM, Fields, Christopher J <cjfields at illinois.edu
> wrote:

>  Depending on the bioperl components, you could make it more specific as
> well.  For instance, I wouldn't have a problem focusing on such code if it
> turns out to be a significant bottleneck (even to the point where we move
> it to a separate repo, a'la Bio::FeatureIO).
>
>  chris
>
>  On Mar 5, 2014, at 7:49 AM, Abigail Cabunoc <Abigail.Cabunoc at oicr.on.ca>
> wrote:
>
>   Hi everyone,
>
>  I proposed the WormBase visualization project and am listed as the
> potential mentor. The 'some perl' is for the back-end of our webapp (custom
> perl code - using BioPerl in some parts) since I'm not sure we have the
> correct endpoints in our API for this kind of visualization. If we want to
> keep the project more general, I can remove the perl component from the
> scope of the project.
>
>  Abby
>
> ---------- Forwarded message ----------
> From: Eric Talevich <eric.talevich at gmail.com>
> Date: Mon, Mar 3, 2014 at 11:34 PM
> Subject: Re: [GSoC] GSOC OBF & GMOD
> To: Amelia Ireland <amelia.ireland at gmod.org>
> Cc: "Fields, Christopher J" <cjfields at illinois.edu>, Robin Haw <
> robin.haw at oicr.on.ca>, "gsoc at lists.open-bio.org" <gsoc at lists.open-bio.org>,
> Pjotr Prins <pjotr2014 at thebird.nl>, Toby Hocking <tdhock5 at gmail.com>
>
>
>  Hi everyone,
>
>  I would like to suggest these GMOD projects as being suitable for
> collaboration with OBF:
>
> = JBrowse: REST daemon for Chado =
>  http://gmod.org/wiki/GSoC#JBrowse:_REST_daemon_for_Chado
>
>  All of the Bio* core projects are in server-friendly languages, and
> CHADO support would likely be a useful component in any of the Bio*
> libraries. Has anyone on the GMOD side volunteered to mentor this project?
>
>
>
> = Galaxy CloudMan =
> http://gmod.org/wiki/GSoC#Galaxy_CloudMan
>
>  The idea itself is very cool. It doesn't directly require new
> development on any of the existing Bio* projects, as I understand it, but
> several of the Biopython devs in particular are actively using and/or
> involved with Galaxy, so we could offer informal support at the very least
> to students working on this project. I see the Galaxy core devs have
> volunteered to mentor, so students would be taken care of.
>
>
> = Galaxy Charts and Open Requests =
> http://gmod.org/wiki/GSoC#Galaxy_Charts_and_Open_Requests
>
>  Similar rationale. This idea looks flexible enough to accommodate some
> other ideas out there.
>
>
> = WormBase: data visualization =
> http://gmod.org/wiki/GSoC#WormBase:_data_visualization
>
>  This is another flexible idea that students can adapt to match their
> interests. When you say "some Perl", is that BioPerl, or Wormbase-specific
> CGI code? I can envision this project yielding some reusable Javascript
> components, too -- has BioJS shown any interest in collaborating?
>
>
> We have another potential project mentor who has proposed developing a
> visualization tool for copy number variation (Toby CC'd here; we'll follow
> up on this), and Galaxy Charts, JBrowse or GBrowse might be a good platform
> for developing that.
>
>
>  If you agree these ideas are worthy of OBF-ification and the listed
> mentors are still interested in seeing these projects through with OBF,
> I'll copy the items from GMOD's GSoC ideas page to OBF's equivalent:
>  http://www.open-bio.org/wiki/Google_Summer_of_Code_2014_Ideas
>
>  Cheers,
> Eric
>
>
>  On Mon, Mar 3, 2014 at 2:16 PM, Amelia Ireland <amelia.ireland at gmod.org>
> wrote:
>
>>  Perhaps the best thing would be if some OBF folks had a look at the
>> proposals that the Genome Informatics group have put together and assessed
>> which would be most amenable to OBF-ification? I think that is a better
>> approach than trying to coerce the ideas that Robin and I picked into
>> being
>> OBF projects.
>>
>> Here is the list:
>>
>> http://gmod.org/wiki/GSoC
>>
>> Thanks,
>> Amelia.
>>
>>
>>
>> On Thu, Feb 27, 2014 at 2:15 PM, Fields, Christopher J <
>> cjfields at illinois.edu> wrote:
>>
>> > On Feb 27, 2014, at 3:04 PM, Pjotr Prins <pjotr2014 at thebird.nl> wrote:
>> >
>> > > On Thu, Feb 27, 2014 at 07:46:01PM +0000, Fields, Christopher J wrote:
>> > >> Ah yes, but then I believe Amelia?s point is whether this is
>> something
>> > that the Biojavascript folks (who aren?t officially one of the OBF Bio*
>> but
>> > have been accepted as their own GSoC org) might be a better fit.  Which
>> > very well could be ?yes? depending on their view of things.  Maybe
>> someone
>> > can reach out to them and ask?
>> > >
>> > > If you read the BioJS paper, you'll see that they are mostly working
>> > > on visualisation components for the browser.
>> > >
>> > > We are talking Client-server here - different ball game. If we were to
>> > > start a serious project in Javascript we should talk about that. We
>> > > should not fear mixing programming languages. We have gotten beyond
>> > > that point by now. I currently write code in Ruby, D, Python and
>> > > Javascript. Apparently LISP I can't get around either. I don't think I
>> > > am that special. Main thing is to find mentors that take an active
>> > > interest in maintaining such a code base. Without a mentor we won't
>> > > get anywhere.
>> > >
>> > > Javascript + Nodejs makes a pretty enticing server environment, these
>> > > days. And more and more students are learning Javascript before Perl
>> > > or Python. Now if there is an eager mentor...
>> > >
>> > > Pj.
>> >
>> > I'm not disagreeing, actually.  I just want to make sure these go to the
>> > right place, whether it be OBF or elsewhere.
>> >
>> >
>> > chris
>>
>>
>>
>>
>>  --
>> Amelia Ireland
>> GMOD Community Support
>> Generic Model Organism Database project
>> http://gmod.org || @gmodproject
>>   _______________________________________________
>> GSoC mailing list
>> GSoC at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/gsoc
>>
>
>
>
>
>  --
> Amelia Ireland
> GMOD Community Support
> Generic Model Organism Database project
> http://gmod.org || @gmodproject
>
>
>