[Biopython-dev] GSoC genomic variant proposal

[Lenna Peterson]

Hi all,

I realize time is short, but I am still in the planning phase of my
GSoC proposal! I wanted to take a moment to formally introduce myself
to the dev list.

I am affiliated with Purdue University, located in Indiana, USA and
best known for engineering (Neil Armstrong is a famous graduate). I
hold a bachelor of arts in biology from Mount Holyoke College in
Massachusetts. I have extensive wet lab experience with genetics; I'm
currently working in a lab genotyping mice (the research is intestinal
lipid metabolism). In August, I begin a PhD in interdisciplinary life
science at Purdue, and I anticipate that my research will fall
somewhere in the field of bioinformatics/computational biology. I hope
to use biopython extensively!

In my spare time, other than programming, I enjoy ballroom dance,
science fiction novels, board games, and sailing.

I've been programming for about 6 years and using python for 4; other
languages with which I'm familiar include Perl/CGI, HTML/CSS, PHP, SQL
(primarily MySQL and SQLite), and C++/C. I place a high value on
object oriented design and execution.

I understand the basics of formal grammar and have some experience
with lex/flex as well as PLY (python lex/yacc). My work so far with
biopython has been on the CIF parsing module. One of my primary goals
for the genomic variants project would be to implement as much
polymorphism and abstraction as possible, for the benefit of both
users and future developers.

I'm working on a proposal for the genomic variants project, and while
I understand the basics of molecular biology and genetics, I lack
firsthand experience with the type of workflow that would occur in the
context of genomic variants. If anyone can supply a few examples, it
would be greatly appreciated.

I hope to have a proposal draft ready for feedback by Monday.

Regards,

Lenna Peterson
github.com/lennax