[Biopython] New project for Google Summer of Code 2011

[Mikael Trellet]

Hi Eric and Brad,

I gather here my answer to your two mails. First of all, thanks a lot for
your reactivity and your motivation ! I'm going to try to be as complete as
possible. And sorry for the late answer, I promised to a friend of mine to
make some sport with him, a good way to reflect about my answer !!

This looks like a cool project, and I'd be happy to mentor. It is quite
> close to the deadline, so I'd encourage you to register with GSoC and put a
> draft of your application on Melange to reserve your spot in the review
> process:
> http://www.google-melange.com/gsoc/org/google/gsoc2011/obf
>

Just done ! And also, as Joao said, an account on Github, I just have to
make a first proposal draft tonight to avoid wasting time tomorrow morning.

You can link to external documents from your main application. This gives
> you some leeway to add more details during the review process -- put your
> detailed project plan and other supporting info in a Google Doc and just
> give us the link.


I haven't some big project to share with you right now, but I should find
again my python project from last year later in the evening. It was a very
specific project, dealing with huge files and having as purpose to calculate
some statisitcs on a particular database linked to genetic data. I can also
show you some simple scripts I did last months for my daily work. One of
them use the PDB parsing module. It's not a complicated one but could give
you an idea. Again as Joao advised me, I will create a diffrent repository
om my new github account.

Biopython serves better as a collection of tried-and-true methods and
> algorithms than as a forum for new methods. Is your project implementing a
> method that's fairly stable and widely accepted, or is this new research or
> your own?


If this work would potentially be the foundation for a lot of other
> computational experiments, new tools, etc., rather than one approach to
> solving a broad problem (which could become obsolete later), that should be
> emphasized.


I'm sorry, perhaphs I misexplained myself, there wouldn't be any complicated
calculations. It would be only information and statistics extraction from
the PDB, allowing to the user, afterward and independently, more complicated
calculations.

- Your timeline has good details in it and you should align these
>  with the coding weeks, so you have a week by week description of
>  what you plan to accomplish:


I'm working on it, should be done also tonight ;)

Thanks again for your attention, don't hesitate if you have other questions
or remarks, I think I will give you some news shortly,

Cheers,

Mikael