[Biopython-dev] Gsoc 2014 aspirant

[Harsh Beria]

The pairwise alignment project is not listed in the Ideas page. If I work
on it and make a GUI or command line frontend, can that be taken up as a
GSOC project? Who can be the potential mentor for this project so that I
can chalk out the details before starting to code? Also, do I need to add
the project on the idea page?


On Sat, Mar 1, 2014 at 12:40 AM, Harsh Beria <harsh.beria93 at gmail.com>wrote:

> I can work on pairwise sequence alignment. Actually, I have previously
> worked on this using Dynamic programming. But I doubt whether this can be a
> GSOC project because the work load will not be too much. If we use
> different methods to predict sequence alignment and make a front-end which
> allows the user to input the sequence or even a pdb file and method of
> alignment and predict the alignment, the work can be substantial enough.
>
> Also, as suggested by Christopher, sequence alignment is pretty basic and
> we can use C backend, which can significantly improve the runtime. So, we
> can discuss it and I can start working on it.
>
>
> On Fri, Feb 28, 2014 at 11:15 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
>
>> I'm wondering, with something that is as broadly applicable as pairwise
>> alignment, would it be better to implement only in Python (or implement in
>> Python wedded to a C backend)?  Or maybe set up something in python that
>> taps into an already well-defined C/C++ library that does this?
>>
>> The reason I mention this: with bioperl we went down this route with
>> bioperl-ext a long time ago (these are generally C-based backend tools with
>> a perl front-end), that bit-rotted simply b/c there were other more
>> maintainable options.  IIUC from this post, similar issues re:
>> maintainability held for Bio/pairwise2.py (unless I'm mistaken, which is
>> entirely possible).  However, tools like pysam and Bio::DB::Samtools (on
>> the perl end) seem to have been maintained much more readily since they tap
>> into a common library.
>>
>> For instance, my suggestion would be to implement a Biopython tool that
>> does pairwise alignment using library X (SeqAn, EMBOSS, etc).  Or maybe a
>> generic python front-end that allows users to pick the tool/method for the
>> alignment, with maybe a library binding as an initial implementation.
>>
>> chris
>>
>> On Feb 28, 2014, at 4:07 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>>
>> > Hi Harsh Beria,
>> >
>> > One option is to work on pairwise sequence alignments. Currently there
>> is some code for that in Biopython (in Bio/pairwise2.py), but it is not
>> general and is not being maintained. This may need to be rebuilt from the
>> ground up.
>> >
>> > Best,
>> > -Michiel.
>> >
>> > --------------------------------------------
>> > On Wed, 2/26/14, Harsh Beria <harsh.beria93 at gmail.com> wrote:
>> >
>> > Subject: [Biopython-dev] Gsoc 2014 aspirant
>> > To: biopython at lists.open-bio.org, biopython-dev at lists.open-bio.org,
>> gsoc at lists.open-bio.org
>> > Date: Wednesday, February 26, 2014, 11:14 AM
>> >
>> > Hi,
>> >
>> > I am a Harsh Beria, third year UG student at Indian
>> > Institute of
>> > Technology, Kharagpur. I have started working in
>> > Computational Biophysics
>> > recently, having written code for pdb to fasta parser,
>> > sequence alignment
>> > using Needleman Wunch and Smith Waterman, Secondary
>> > Structure prediction,
>> > Henikoff's weight and am currently working on Monte Carlo
>> > simulation.
>> > Overall, I have started to like this field and want to carry
>> > my interest
>> > forward by pursuing a relevant project for GSOC 2014. I
>> > mainly code in C
>> > and python and would like to start contributing to the
>> > Biopython library. I
>> > started going through the official contribution wiki page (
>> > http://biopython.org/wiki/Contributing)
>> >
>> > I also went through the wiki page of Bio.SeqlO's. I
>> > seriously want to
>> > contribute to the Biopython library through GSOC. What do I
>> > do next ?
>> >
>> > Thanks
>> > --
>> >
>> > Harsh Beria,
>> > Indian Institute of Technology,Kharagpur
>> > <http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com
>> > _______________________________________________
>> > Biopython-dev mailing list
>> > Biopython-dev at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biopython-dev
>> >
>> > _______________________________________________
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>>
>>
>
>
> --
>
> Harsh Beria,
> Indian Institute of Technology,Kharagpur
>  <http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com
>
>  Ph: +919332157616
>
>


-- 

Harsh Beria,
Indian Institute of Technology,Kharagpur
<http://www.iitkgp.ac.in/>E-mail: harsh.beria93 at gmail.com

Ph: +919332157616