[GSoC] GSoC and SciRuby (was: Re: Project Proposal for Google Summer of Code)

[Peter Cock]

Thanks John,

That sounds very positive. I hope some of the BioRuby team
take up your invitation. In addition to leading the OBF GSoC
application this year, Raoul is also one of the BioRuby core
team - so I'm sure he will pass on your message.

Regards,

Peter

---------- Forwarded message ----------
From: John Woods <john.woods at marcottelab.org>
Date: Tue, Mar 3, 2015 at 6:03 PM
Subject: GSoC and SciRuby (was: Re: [GSoC] Project Proposal for Google
Summer of Code)
To: Peter Cock <p.j.a.cock at googlemail.com>, Joshua Klein <mobiusklein at gmail.com>
Cc: OBF GSoC <gsoc at mailman.open-bio.org>


I can't help with the Py projects, but if there are any Ruby projects,
it's possible SciRuby can adopt them. (Please consider this an
invitation.)

Here are some basic criteria:

Project ideas should have an immediate user. I don't think we should
be writing code as part of GSoC that someone isn't going to be making
use of for research right now. I want our students to be able to get
feedback from users, not just reviewers.
Project ideas should be infrastructure-related. It's okay if they're
biological rather than general science, but there should be a general
application to the work. In other words, don't just write a sequencing
pipeline. Write a general-purpose pipeline with a sequencing example
application. Or better yet, have the student write the general
pipeline, and have the mentor write the biological application — this
way the student is getting feedback from an actual user.
Project ideas must have a mentor. We never have enough mentors.
Mentors must be involved enough to post the idea on the page and must
be involved in reviewing students. Unresponsive mentors will be
dropped along with their projects.

Here is our ideas page, where you may post your idea:
https://github.com/SciRuby/sciruby/wiki/Google-Summer-of-Code-2015-Ideas

Please especially note the part about "Recommended skills" before you
write up your idea.

We're especially interested in getting some female mentors involved,
but the approach we used last year didn't work.

John

On Tue, Mar 3, 2015 at 11:11 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Hi Joshua,
>
> Thank you for you interest. Unfortunately we've just heard that
> the  Open Bioinformatics Foundation (OBF) was not accepted
> into the Google Summer of Code 2015 programme:
>
> http://news.open-bio.org/news/2015/03/sadly-obf-not-accepted-for-gsoc-2015/
>
> It may be possible to pursue your project idea with one of the
> accepted organisations (perhaps the Python Software Foundation)
> by including a mentor from Biopython. We've not yet approached
> any of the other potential partner organisations yet though.
>
> Good luck,
>
> Peter
>
>
>
> Peter
>
>
> On Tue, Mar 3, 2015 at 2:58 AM, Joshua Klein <mobiusklein at gmail.com> wrote:
> > Hello,
> >
> > I've been working on a python library for reading, writing, and manipulating
> > glycan structures and glycomics data. One of my collaborators suggested I
> > inquire here if this might be of interest to the Biopython team and if it
> > was not too late to apply for a Google Summer of Code sponsorship.
> >
> > The library can currently do the following:
> >
> > Read and write GlycoCT Condensed format carbohydrate structures that are
> > concrete (having no variable or undefined structures)
> > Read GlycoCTXML format carbohydrate structures that are concrete
> > Manipulate the tree structure, adding and removing monosaccharide and
> > substituent nodes, as well as altering existing nodes.
> > Calculate elemental compositions for glycan structures
> > Create arbitrary chemical derivitizations (e.g. permethylation) of glycan
> > structures
> > Generate B, C, Y, and Z fragments from structures as observed when analyzing
> > a structure with tandem mass spectrometry.
> > Make API calls against GlycomeDB to download structures and annotations on
> > the fly
> > Perform sub-tree inclusion and maximum common substructure searches with
> > fuzzy matching.
> > Plot glycan structures using the Consortium for Functional Glycomics symbol
> > nomenclature with matplotlib.
> > Perform error tolerance name inference on monosaccharides
> >
> > I am currently working on adding support for A and X cross-ring fragment
> > generation and adding other serialization formats such as IUPAC and
> > GlycoMinds Linear Codes.
> >
> > Currently, all of the features are implemented purely in Python.
> >
> > What other information, if any, can I provide?
> >
> > Thank you,
> > Joshua Klein
> >
> > _______________________________________________
> > GSoC mailing list
> > GSoC at mailman.open-bio.org
> > http://mailman.open-bio.org/mailman/listinfo/gsoc
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