New measures of genetic differentiation
Lou Jost has pretty neat paper out describing new measures genetic diversity that accurately account for allelic differences. I've written some PYTHON scripts to parse genepop files, measure allele frequencies, and generate [some of] these measures of diversity. Enjoy.
http://www.ngcrawford.com/django/jost/
Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology,17(18), 4015 - 4026
WordPress Update Issue (and fix)
Using the 'Automatic' update button I got the following error:
Fatal error: Cannot redeclare pclziputilpathreduction()...
To fix this I had to turn off the 'Wordpress Automatic Upgrade Plugin' that was formerly required for automatic updates. More details here.
Olivia Judson Likes Papers.app too!
Now Papers has been reviewed by the New York Times. Sweet.
For me, well, a few days after discovering Papers, I put 20 sacks of real paper into the recycling bin. At last, I’m back to knowing what I have and where it is.
Via the New York Times
How to emulate Blast’s “Short Sequence Parameters”
I just spent an hour figuring out how to emulate Blast's "Short Sequence Search Parameters" in BioPython 1.48. To use PAM30 as your matrix you must use existence and extension parameters (e.g. gap costs) of 9 and 1.
Here's what I've currently got:
PYTHON Quick Links
I write a lot of code using the PYTHON Programing Language. I just gave a very brief overview to a friend who has to learn it this summer. In the course of this lesson, it occurred to me that a lot of the bioinformatic resources that I use every day are not collected in one place. So I've listed a couple of the most useful modules/packages below:
- BioPython
- This package lets you interface with NCBI, parse datafiles (e.g. fastas, Genbank, blast output etc.), run blast queries, run clustalw, etc.
- SciPy
- N-dimensional array manipulation
- MatPlotLib
- Graphing.
- Python DB API
- Database integration
- Google App Engine
- Free webhosting of python cgi scripts. It's in beta.
- Django
- Python Web Application Development package. It can be used in conjunction with Google App Engine.
Here are a few addition sites that I find useful:
- Python 2.5 Quick Reference
- both html and PDF versions are available for free!
- TextMate
- OS X text editor. It's not free, but there is a student discount available
- Forklift
- OS X ftp program. Also not free, but reasonably priced.
Anolebase.org
Right now AnoleBase points here, but I'll have a blog setup for it in the next week or two. I hope to have something like stellabase.org or flybase.org put together by mid spring/early summer.
“Rambo” meets “Snakes on a Plane”
A new installment of the venrable Rambo franchise is being released in January. I'm not much of Stallone fan, but I'm secretly psyched...
But Rambo, who lives a solitary, simple life in the mountains and jungles fishing and catching poisonous snakes to sell, has long given up fighting, even as medics, mercenaries, rebels and peace workers pass by on their way to the war- torn region.
Hell yeah!
Night at the Creation Museum
Excellent Scientific American Article with Answers to Creationist Arguements
Scientific American: 15 Answers to Creationist Nonsense
SA byline: "Opponents of evolution want to make a place for creationism by tearing down real science, but their arguments don't hold up"
NGC byline: This will save me some time at our next family reunion.
