[Biopython-dev] [GSoC] Project Proposal for Google Summer of Code

[Peter Cock]

Thanks Joshua,

Outside GSoC, adding glycoinformatics to Biopython sounds interesting.
As far as I know none of our existing contributors do much in this area,
so our feedback may be limited to Python style (PEP8 please) and
practicalities like unit tests and documentation.

We should probably also ask on the main Biopython mailing list - that
might reveal some potential users of the code?

Is your code public already? e.g. GitHub or Bitbucket?

Are there any pre-existing licences associated with your code? Can
you simply adopt the Biopython Licence? This like the MIT/BSD
licence in spirit (indeed we're considering moving to the 3-clause
BSD licence as that is more mainstream).

After a brief debate about appropriate namespace(s), I would suggest
you fork our repository and work on a branch...

Regards,

Peter

On Tue, Mar 3, 2015 at 5:05 PM, Joshua Klein <mobiusklein at gmail.com> wrote:
> I am sorry to hear that the OBF did not make it in this year. We are still
> interested in finding out if the Biopython team is interested in including
> glycomics tools in the core library, or in some other looser association.
> Real glycoinformatics is relatively inaccessible outside of two titanic Java
> libraries, which doesn't jive with how a lot of modern bioinformatics is
> done today.
>
> Thank you,
> Joshua Klein
>
> On Tue, Mar 3, 2015 at 10:25 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
>
>