[GSoC] GSOC OBF & GMOD

Tue Mar 4 20:02:26 UTC 2014

I know the gmod folks don't want to split up too much, but the reactome projects might fit into a systems bio org.  IIRC there was one accepted but can't think of it offhand...

Chris

Sent from a Phone of Ingenuity (+3)

-------- Original message --------
From: Eric Talevich
Date:03/04/2014 1:34 AM (GMT-06:00)
To: Amelia Ireland
Cc: "Fields, Christopher J" ,Robin Haw ,gsoc at lists.open-bio.org,Pjotr Prins ,Toby Hocking
Subject: Re: [GSoC] GSOC OBF & GMOD

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 || @gmodproject
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