[GSoC] Project Proposal for Google Summer of Code

[Joshua Klein]

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:

   1. Read and write GlycoCT Condensed format carbohydrate structures that
   are concrete (having no variable or undefined structures)
   2. Read GlycoCTXML format carbohydrate structures that are concrete
   3. Manipulate the tree structure, adding and removing monosaccharide and
   substituent nodes, as well as altering existing nodes.
   4. Calculate elemental compositions for glycan structures
   5. Create arbitrary chemical derivitizations (e.g. permethylation) of
   glycan structures
   6. Generate B, C, Y, and Z fragments from structures as observed when
   analyzing a structure with tandem mass spectrometry.
   7. Make API calls against GlycomeDB to download structures and
   annotations on the fly
   8. Perform sub-tree inclusion and maximum common substructure searches
   with fuzzy matching.
   9. Plot glycan structures using the Consortium for Functional Glycomics
   symbol nomenclature with matplotlib.
   10. 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/gsoc/attachments/20150302/0f0c1244/attachment.html>