[bip] SciPy 2007 - Birds of a Feather - Biology

[Titus Brown]

On Sat, Aug 18, 2007 at 12:17:46AM +0100, Nathan Harmston wrote:
-> and Brandon wrote:
-> >    1. Need to establish python/biology community, via website,
-> >   biology-in-python mailing list, rss, blogs, etc.
-> 
-> That would be a great idea, it think it would be great to be able to post
-> code/solutions and get it reviewed. Peer-review of tools could be a great
-> way of finding bugs in code and better ways of doing things that are been
-> done.

Yes!

-> > I have agreed to setup the python/biology community site. There are some
-> > ideas in the notes below and I will also be posting ideas and requesting
-> > ideas for this in a future post.
-> >
-> 
-> How about a trac/wiki with some kind of dpaste sort of functionality?

Yes, this is the plan.  (Note to others -- by 'dpaste' Nathan means
something like http://dpaste.com/, a pastebin for posting code
examples.)  For now, I suggest that code be posted here or (eventually)
on the Wiki -- if it becomes too much we can install a pastebin site.

-> > Other people's databases.
-> 
-> How about defining something using sqlalchemy, I know people dont use
-> BioSQL, but maybe a BioSQL/sqlalchemy api or how about writing a
-> PyEnsembl..would this be a good way to start, might even convince some Perl
-> people to convert.

I brought this up, and what I actually meant was "NCBI" or other such
dbs ;).

-> I think testing should also be able to be hosted.......I think this could be
-> a good way of "proving" that  the results are "ok" (notice the quotes).

Yes, this will probably devolve onto me or Brandon for now.  We're very
interestd in this kind of stuff.

-> Documentation of any core set of modules needs to be very good.

Yeah, that's what's holding us (Chris Lee + me) from posting our current
interface spec for discussion.  Sorry, we will post, err, any day now...
;)

cheers,
--titus