[Biopython-dev] [GSoC] Gsoc 2014 aspirant

[Harsh Beria]

Hi,

Regarding the algorithm part of Pairwise Sequence Alignment, I can use
Dynamic Programming (Smith Waterman for local and Needleman Wunsch for
Global Alignment). Please suggest if I should go for dynamic programming.

Also, the above discussion points out that the implementation should be
purely python based for cross-platform compatibility.


On Thu, Mar 6, 2014 at 7:19 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:

> Hi Nigel,
>
> While compiling Biopython on Windows can be tricky, in my experience it
> has been easy to compile the C libraries in Biopython on other platforms
> (Unix/Linux/MacOSX). Have you run into specific problems compiling
> Biopython? I would think that wrapping 3rd-party libraries or executables
> is much more error-prone.
>
> Best,
> -Michiel.
>
> --------------------------------------------
> On Tue, 3/4/14, Nigel Delaney <nigel.delaney at outlook.com> wrote:
>
>  Subject: Re: [Biopython-dev] [GSoC] Gsoc 2014 aspirant
>  To: "'Peter Cock'" <p.j.a.cock at googlemail.com>, "'Fields, Christopher
> J'" <cjfields at illinois.edu>
>  Cc: biopython-dev at lists.open-bio.org, "'Harsh Beria'" <
> harsh.beria93 at gmail.com>
>  Date: Tuesday, March 4, 2014, 5:39 PM
>
>  As a quick $0.02 from a library user
>  on this.  Back in 2006 when I first
>  started using biopython I was working with Bio.pairwise2,
>  and learned that
>  it was too slow for the task at hand, so wound up switching
>  to
>  passing/parsing files to an aligner on the command line to
>  get around this,
>  as (on windows back then), I never got the compiled C code
>  to work properly.
>  Although pypy may be fast enough and has been very
>  impressive in my
>  experience (plus computers are much faster now), I think
>  wrapping a library
>  that is cross platform and maintains its own binaries would
>  be a great
>  option rather than implementing C-code (I think this might
>  be what the GSoC
>  student did last year for BioPython by wrapping Python).
>
>  Mostly though I just wanted to second Peter's wariness about
>  adding C-code
>  into the library.  I have found over the years that a
>  lot of python
>  scientific tools that in theory should be cross platform
>  (Stampy, IPython,
>  Matplotlib, Numpy, GATK, etc.) are really not and can be a
>  huge timesuck of
>  dealing with installation issues as code moves between
>  computers and
>  operating systems, usually due to some C code or OS specific
>  behavior.
>  Since code in python works anywhere python is installed, I
>  really appreciate
>  the extent that the library can be as much pure python as
>  allowable or
>  strictly dependent on a particular downloadable binary for a
>  specific
>  OS/Architecture/Scenario.
>  _______________________________________________
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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