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

[Peter Cock]

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
>
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