[GSoC] GSOC OBF & GMOD

Wed Mar 5 14:33:15 UTC 2014

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<mailto: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<mailto: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<mailto:amelia.ireland at gmod.org>>
Cc: "Fields, Christopher J" <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>, Robin Haw <robin.haw at oicr.on.ca<mailto:robin.haw at oicr.on.ca>>, "gsoc at lists.open-bio.org<mailto:gsoc at lists.open-bio.org>" <gsoc at lists.open-bio.org<mailto:gsoc at lists.open-bio.org>>, Pjotr Prins <pjotr2014 at thebird.nl<mailto:pjotr2014 at thebird.nl>>, Toby Hocking <tdhock5 at gmail.com<mailto: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<mailto: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<mailto:cjfields at illinois.edu>> wrote:

> On Feb 27, 2014, at 3:04 PM, Pjotr Prins <pjotr2014 at thebird.nl<mailto: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<http://gmod.org/> || @gmodproject
_______________________________________________
GSoC mailing list
GSoC at lists.open-bio.org<mailto: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<http://gmod.org/> || @gmodproject