[GSoC] GSOC OBF & GMOD

[Eric Talevich]

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
>