[BioPython] Questions & suggestions

[Brad Chapman]

Hi Thomas;

> I recently moved to a new position and of course immediately started
> to convert my colleagues to (Bio)Python :-). One of the most often asked 
> questions with respect to Biopython here is "Does Biopython have the same 
> functionalities as Bioperl?". Is there a document somewhere that compares 
> BioPerl and BioPython? Would be REALLY useful. 

No, not that I know of. Honestly, I am not a big fan of
BioPerl/Biopython comparisons just as I'm not a huge fan of
Perl/Python comparisons -- I'm all for sticking with what you like
and working with it. But definitely if it were useful to people
looking at the projects, I'd be for having that kind of document.

> Another question: is anybody using BioPerl from BioPython? 
> If so, how? BioCorba?

BioCorba is for all intensive purposes dead. The code still works
and all but it was not really being used and I've stopped doing
development on it (so I can graduate and all :-).

> And then some suggestions: I think it's time to do something about the 
> Biopython documentation, and maybe remove some obsolete, incomplete and/or 
> unmaintained code. At the moment it's a bit difficult to get a good overview 
> of what is present and useable in Biopython, I think... 

Agreed. About the docs -- as I mentioned the other day, I'm planning
to factor out the Tutorial into smaller cookbook-style sections
(there is a directory in CVS -- Doc/cookbook, that I've started
populating). For this weekend I have in my head to pull out at least 
the "Working with sequences" section thanks to the feedback I got
from Marc, and to pull out and update the Bio.db registries section.

I'd certainly welcome help on this front -- from yourself and anyone
else. Taking it as quick as it'll go but that's my current plan to
keep the useful docs and fix them to be up to date as possible.

If you are talking to beginners in Python, it might also be nice to
point them to Katja and Catherine's course:

http://www.pasteur.fr/recherche/unites/sis/formation/python/

which is linked from the documentation page. This does have a lot of
very nice code and explanations for getting started.

As far as code goes -- if you have suggestions for modules that are
no longer useful and we don't think can be fixed/updated easily
please do suggest a plan of action. We can get a survey on whether
others use these modules and then decide where to go. It's always a
good idea to keep out cruft.

> Brad, I vaguely remember that you mentioned something about replacing 
> HappyDoc? I'd be happy to help out.... 

Yeah, I will also play around with that this weekend. But, I do
think the number one priority on the doc front is extracting the
Tutorial into smaller sections. If you want to help on that, it
would be great. For instance, the PDB module could have it's own
documentation section :-).

Thanks for the comments -- I'd be interested to know what others
think about the plans, and also very interested in others picking a
section of the Tutorial to work on :-).

Thanks-for-the-PDB-updates-as-well-ly yr's,
Brad