[Biopython] Introduction

[Chintalagiri Shashank]

Hello,

I'm an undergraduate student of Physics, from the Indian Institute of 
Technology, Kanpur, and am interested in applying to BioPython for this year's 
Google Summer of Code. My interest in biology in the context of my Major is a 
somewhat complex and long-winded explanation, the basis of which is that for 
the last couple of years I've been seriously looking into biology 
(specifically, Structural Biology within the context of elements from 
Bioinformatics and certain other fields) as a potentially interesting field of 
study, and have been doing courses about the same. 

I was initially toying with the idea of attempting to write a sequence 
analysis 'framework' of sorts, where I could have the scaffolding to play 
around with simple algorithms for structure prediction. In retrospect, I 
should have make a more thorough search which should have led to OBF and 
BioPython, but as it is the idea went into cold storage due to certain other 
pressing constraints on my time, specifically a time-bound institute project 
that was behind on its schedule. 

I found OBF soon after the initial GSoC organizations announcement, and have 
since been looking over various pieces of documentation on it. I did look at 
the bugtracker as well, as was suggested on list, but it seemed to me that a 
lot of the bugs listed there were patches awaiting review. I do intend to take 
another look at the list and see if there is anything I can do there, but I 
decided that I shouldn't wait any longer before introducing myself formally on 
the list.

I'm interested in working on BioPython/PyCogent interop, because I see a lot 
of potential in tying the two toolkits together and doing so before more 
wheels are reinvented. The ability to look at evolutionary effects and 
structural effects simultaneously could be quite interesting. To be fair, I 
must note here that while I am quite at home with Python and have a working 
understanding of the elements that make up BioPython, I have no production 
experience with either toolkits, and do not have a theoretical understanding 
of the evolutionary algorithms behind pyCogent. However, I am confident that I 
will be able to pick up the necessary skills over time, atleast to a degree 
necessary to make interoperability possible. 

I also have a couple of ideas in mind for BioPython projects, which really 
aren't well fleshed out yet. I'll think about them, specifically, their need 
and feasibility, and send the details to the list in a few days. 

Please do let me know if you would like any more information in the meanwhile. 
I've been on the mailing list for a couple of weeks now, so you can just reply 
on-list unless there is a need for off-list communication. 

Regards
Chintalagiri Shashank

chintal at iitk.ac.in