[Biopython] GSoC Application: "Representation and manipulation of genomic variants"

[Chaitanya Talnikar]

Hi,
I, Chaitanya Talnikar, am a third year Undergraduate student of
Chemical Engineering at Indian Institute of Technology. I would like
to work on the project "Representation and manipulation of genomic
variants".

As I understand this project is on human genomic variations and
constructing a representation of the variations that would account for
most of the variation file formats. I would like to how much should I
write in the proposal. Would a description of the internal
representation be sufficient?

Talking about my experience, I have a good grasp of python. I have
done courses on Molecular Biology and Computational Biology in which I
learnt the sequence alignment algorithms and the classification of
proteins based on hidden markov models of insertion, deletion and
mutations in proteins. I have used bioinformatics in the projects that
I've done in the field of systems biology and made extensive use of
NCBI blast and other utilities.

I have worked on several projects related to programming. Some of
projects whose code is online are:
LTanks (http://code.google.com/p/ltanks/)
This is a clone of a windows game. It has had around 200 downloads.
OffApt (http://code.google.com/p/offapt/)
This is a software that allows people to download ubuntu packages from
windows, it includes a dependency resolver for debs and also a
downloader. This project required a lot of file parsing and string
manipulations
I've mainly used python to solve the mathematical problems at
http://projecteuler.net