[Biopython] New project for Google Summer of Code 2011

[Eric Talevich]

Hi Mikael,

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

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.

Thoughts on the current proposal:

 - 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.

 - Calculating binding affinity from physico-chemical properties sounds
computationally intensive. Is Python the most appropriate language for
implementing it? Would this wrap a high-performance library, or use Numpy
very efficiently?

 - As Brad just mentioned -- you've written scripts in Python; can you make
any of these public? Also, the sooner you can create an account on GitHub
and get up to speed with our build system (it's nothing tricky), the better.

I'm sure João has filled you in on the process, but if you have any other
questions feel free to ask here.

Cheers,
Eric


On Thu, Apr 7, 2011 at 9:49 AM, Mikael Trellet <mikael.trellet at gmail.com>wrote:

> Dear all,
>
> My name is Mikael and I'm a french student, currently working in the
> Netherlands. I was informed few days ago about the close deadline for
> Google
> Summer of Code project submission. I'm aware that my project comes a bit
> late but I would like to propose you it, and have your point of view, even
> your advices. It's a project about which I think for few weeks, and the GSC
> would seem a good way to develop it. You will find everything about the
> project and my background in the attached document.
>
> Thanks in advance for your remarks and the time you'll give me,
>
> Cordially,
>
> --
> Mikael TRELLET,
> Computational structural biology group, Utrecht University
> Bijvoet Center,
> The Netherlands
>
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