Nick Crawford Evolution and more…

17Dec/080

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

Filed under: Blog No Comments
27Oct/080

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:

  1.  result_handle = NCBIWWW.qblast(
  2.     "blastp",
  3.     "nr",
  4.     seq_record.seq.tostring(),
  5.     matrix_name = 'BLOSUM62',
  6.     word_size='2',
  7.     expect='30000',
  8.     gapcosts ='9 1',
  9.     composition_based_statistics='no adjustment')
Tagged as: , , No Comments
14May/081

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.
Tagged as: 1 Comment
7Dec/070

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.

Filed under: Blog No Comments
1Dec/070

“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!

Filed under: Blog No Comments
8Oct/070

802

You need to a flashplayer enabled browser to view this YouTube video

Filed under: Blog No Comments
7Oct/070

Night at the Creation Museum

You need to a flashplayer enabled browser to view this YouTube video

Filed under: Blog No Comments
26Feb/070

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.

Filed under: Blog No Comments
6Feb/070

Bill’s Bean Dip

This is my pal Bill's awesome bean dip recipe. I made this for the SuperBowl. It's addictive and very fattening. Not a good combination if you're trying to lose weight. But, it's so worth it. Mmm...

  • 1/2 block of Velveta (looks like ~2 sticks of butter)
  • 1 jar of salsa. Bill recommends the "Pace Medium Salsa."
  • 1 can of Black Beans (aka. Frijoles Negros). Don't forget to drain them!
  • 1 can of chili. Vegetarian works great.

Combine all the ingredients in a sauce pan and simmer until the cheese melts. For the best flavor this should take ~ 15 mins.
Serve with lots of Tortilla chips. Try not to gorge yourself.

Filed under: Blog No Comments
24Jan/070

Population Genetics Review

I came across this really nice post by Razib on his Gene Expression blog. It's a quick and dirty review of all those population genetics equations I've started to forget, or in some instances, never properly understood in the first place!

Filed under: Blog No Comments
 « Newer Entries  

RSS OOE: Another blog I help write

  • From Tophat to Pysam July 21, 2010
    I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file.  This meant I need to convert filetypes. So, I fired up sa […]
  • Inferring Heterozygosity from SNP data April 20, 2010
    This looks straightforward.  n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
  • Why we are "Python Fanboys" April 15, 2010
    I think I can safely say that we’re all Python evangelists.  In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is.  Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]

Web Favs via GReader

Evolution

People

Recent Posts

Meta