[Biopython-dev] GSoC: Refining the PDB-Tidy project idea

[Eric Talevich]

Hi GSoC'ers,

The PDB-Tidy idea on Biopython's Summer of Code page seems to have attracted
interest from a number of highly qualified students:
http://biopython.org/wiki/Google_Summer_of_Code#PDB-Tidy:_command-line_tools_for_manipulating_PDB_files

Please, don't let this deter you from applying! Google allocates student
slots to each organization based on the number of applications received, so
if OBF receives more applications, we can accept more students.

However, I'm also concerned that I've made the project description too
general. (Or is it too specific?) This article describes the characteristics
of a well-defined GSoC project idea:
http://en.flossmanuals.net/GSoCMentoring/SelectingProjects

In the interest of improving the opportunities for each student, I'm
suggesting that the proposals that are submitted under the PDB-Tidy theme
focus on a specific goal beyond the manipulation PDB files. At the risk of
being "That Guy", I'll give some examples of what I mean:

(a) Improve interoperability with external tools like AutoDock or Modeller;
(b) Port some MolProbity-like functionality to Biopython;
(c) Improve interoperability and consistency between Bio.PDB and the rest of
Biopython;
(d) Write a parser for some useful format.

Also, would anyone else be interested in co-mentoring one of these projects?
It's good for a GSoC project to have a secondary mentor -- not required, but
helpful -- and I think some support from a more experienced structural
biologist would be valuable here.

Thanks & best regards,
Eric