[Biopython-dev] Fw: GSoC Application

[阮铮]

Sorry I forget to introduce myself.
My name is Zheng Ruan, currently a first year graduate students at the University of Georiga. I have a background in biology and now pursue a PhD in Bioinformatics. I taught myself many programming language and finally python became my favorite. I use biopython a lot for everyday sequence manipulation and format conversion. For example, I use Bio.Phylo class for reroot tree and visualization functionality in the sever http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/index.php, which has just been accepted by NAR. I really hope to contribute the the Open Source Project and GSoC seems to be a good start point. I think the codon alignment proposal suitable to me because it requires medium programming skills and I've already finished the Computational Molecular Evolution by Ziheng Yang and also have a phylogenetics course this spring semester. Thanks for all.


Best,
Zheng Ruan


------------------ Original ------------------
From:  "Zheng Ruan"<rz1991 at foxmail.com>;
Date:  Apr 27, 2013
To:  "biopython-dev"<biopython-dev at lists.open-bio.org>; 

Subject:  [Biopython-dev] GSoC Application



Hi Biopython developers,

I hope it's not too late to inform you my interest in Biopython GSoC, but I talked to Eric Talevich several weeks before that I would like to apply the Codon Alignment proposal. As a simple trial, I've already got a simple implementation of codon alignment script as can be found in https://github.com/zruan/CodonAlignment. It doesn't account for frame shift and mismatches between protein sequences and nucleotide sequences. But as least it works if the protein sequences can be exactly translated by nucleotide sequences. Hopefully I will finish my proposal this week. Is there any suggestions?


Sincerely,
Ruan