[TriZPUG] PyCamp: Pretty Please?

[Chris Calloway]

On 2/9/2010 12:29 PM, Og Maciel wrote:
> Yeah, shortly after posting my message here it hit me that I was
> looking at the 2009 event. The funny things was that I first heard of
> it via a Tweet message that same night and I automatically assumed it
> was an upcoming event. :)

Sorry about that. I've been trying to get our feeds for events and news 
better behaved for Planet. In doing so, the same feeds are picked up by 
our automatic Twitter posting service and I forgot to turn that off 
while I was working. There was some feed trashing while got it right. 
Now that events are tagged to start dates and news items are tagged to 
effective dates, I'm hoping this won't happen again.

> I'm definitely not a beginner but what attracted me to pycamp was not
> the level but that it would be applied in science, which to me is
> still a novelty. Even though I have a BS in biochemistry, I have never
> been in an environment where people were using open source for their
> research...

Python and Perl are now pretty indispensable in biochem research.
BioPerl exceeds BioPython in many areas and has a longer history. But
BioPython has things only it can do and is developing more quickly.

BioPython 1.53 was released this past December 15. Unfortunately, the
hosting for both it and the Open Bioinformatics Foundation (which
sponsors BioPython, BioPerl, BioJava, BioRuby, and a bunch of others)
seems to have had some kind of nuclear meltdown in just today:

http://open-bio.org/

A post today to the BioPython mailing list says it is just temporary
maintenance.

In the meantime, BioPython is a standard Debian package. So just apt-get
install python-biopython.

There is a core of PyMol users here at UNC:

http://www.pymol.org/

ProDaMa is Python protein dataset management that works with BLAST and PDB:

http://iasc2.diee.unica.it/prodama/

BIANA is a pretty sophisticated protein analysis framework for Python:

http://sbi.imim.es/web/BIANA.php

You probably want to check out:

the *3rd Edition* of Python Scripting for Computational Science:

http://www.amazon.com/dp/3540739157/

A Primer on Scientific Programming with Python:

http://www.amazon.com//dp/3642024742

Bioinformatics Programming Using Python:

http://www.amazon.com/dp/059615450X

Jason Kinser's Python for Bioinformatics:

http://www.amazon.com/dp/0763751863

Sebastian Bassi's Python for Bioinformatics:

http://www.amazon.com/dp/1584889292

Bioinformatics Programming in Python:

http://www.amazon.com/dp/3527320946

Any of those would be better for you than an afternoon at PyCamp of,
"This is how NumPy implements the Python array protocol."

-- 
Sincerely,

Chris Calloway
http://www.secoora.org
office: 332 Chapman Hall   phone: (919) 599-3530
mail: Campus Box #3300, UNC-CH, Chapel Hill, NC 27599