Nick's Blog http://www.ngcrawford.com Evolution, Photography, Music, and more... Wed, 24 Sep 2008 11:55:03 +0000 http://wordpress.org/?v=2.6 en PYTHON Quick Links http://www.ngcrawford.com/2008/05/14/python-quick-links/ http://www.ngcrawford.com/2008/05/14/python-quick-links/#comments Wed, 14 May 2008 14:03:32 +0000 Nick http://www.ngcrawford.com/2008/05/14/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:

  • Â 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.
]]> http://www.ngcrawford.com/2008/05/14/python-quick-links/feed/ Anolebase.org http://www.ngcrawford.com/2007/12/07/anolebaseorg/ http://www.ngcrawford.com/2007/12/07/anolebaseorg/#comments Fri, 07 Dec 2007 13:05:48 +0000 Nick http://www.ngcrawford.com/2007/12/07/anolebaseorg/ 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.

]]> http://www.ngcrawford.com/2007/12/07/anolebaseorg/feed/ “Rambo” meets “Snakes on a Plane” http://www.ngcrawford.com/2007/12/01/rambo-meets-snakes-on-a-plane/ http://www.ngcrawford.com/2007/12/01/rambo-meets-snakes-on-a-plane/#comments Sat, 01 Dec 2007 15:55:38 +0000 Nick http://www.ngcrawford.com/2007/12/01/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!

]]> http://www.ngcrawford.com/2007/12/01/rambo-meets-snakes-on-a-plane/feed/ 802 http://www.ngcrawford.com/2007/10/08/802/ http://www.ngcrawford.com/2007/10/08/802/#comments Mon, 08 Oct 2007 17:10:59 +0000 Nick http://www.ngcrawford.com/2007/10/08/802/ [youtube:http://www.youtube.com/watch?v=GL7uW4TYqbs]

]]> http://www.ngcrawford.com/2007/10/08/802/feed/ Night at the Creation Museum http://www.ngcrawford.com/2007/10/07/night-at-the-creation-museum/ http://www.ngcrawford.com/2007/10/07/night-at-the-creation-museum/#comments Sun, 07 Oct 2007 15:30:15 +0000 Nick http://www.ngcrawford.com/2007/10/07/night-at-the-creation-museum/ [youtube:http://www.youtube.com/watch?v=xR8MGAsidFI]

]]> http://www.ngcrawford.com/2007/10/07/night-at-the-creation-museum/feed/ Papers App Review http://www.ngcrawford.com/2007/08/15/papers-app-review/ http://www.ngcrawford.com/2007/08/15/papers-app-review/#comments Wed, 15 Aug 2007 13:17:11 +0000 Nick http://www.ngcrawford.com/2007/08/15/papers-app-review/ I’ve been using Papers, a slick PDF manager, for about 3 months. Papers is like iTunes, but for PDFs. Alas, for those readers still using PC’s Papers is only available for Macs. Additionally it’s primarily designed for biologists; it only has built in PubMed access. If you meet these requirements, it’s a great tool. Additionally, the authors intend to add more journal search services in the future.

Screenshot 01-1

To use Papers you first import your PDFs. This is just a simple matter of drag-n-drop. Then you can go search each paper on PubMed and Papers will import the pertinent metadata (e.g. title, authors, abstract, etc) into its database. Of course you can also use PubMed to search for new articles. In this case, integration is seamless with Papers linking to the PDF and allowing you to download it and the metadata with one click.

Once Papers “knows” about a particular journal you can link straight to it and Papers will provide a list of the 50 most recent articles. Likewise papers provides an authors section with extra fields were you can add their contact information. At the moment this is not integrated with “Address Book,” but again the authors indicate this functionality is in the works. Like the journal search, Papers will also automatically search PubMed for a list of a particular author’s publications.

I do, however, have a few caveats. Papers seems to have issues with very large PDFs (e.g. greater that 50 megabytes) which when opened cause the program to crash. Occasionally, I have problems with the integrated search not finding papers I know I have in my database. A quick restart of the app seems to fix this. Perhaps most importantly, Papers doesn’t yet function as a bibliography/works cited organizer in the manner of EndNote or Sente.

Nevertheless, Papers has proven exceptionally useful while writing my MS thesis. It can now search within PDFs for particular words or phrases. This is helpful when you can not remember where you read about a particular concept. It also allows for reading in PDFs in fullscreen and has note taking functionality. This certainly saves on real paper and reduces clutter on my desk.

Papers is $39 from mekentosj.com and students can get a 40% discount.

]]> http://www.ngcrawford.com/2007/08/15/papers-app-review/feed/ Two Primer Notes In Press: Whiptail Lizards and Hawaiian Trees http://www.ngcrawford.com/2007/06/20/two-primer-notes-in-press-whiptail-lizards-and-hawaiian-trees/ http://www.ngcrawford.com/2007/06/20/two-primer-notes-in-press-whiptail-lizards-and-hawaiian-trees/#comments Wed, 20 Jun 2007 12:04:42 +0000 Nick http://www.ngcrawford.com/2007/06/20/two-primer-notes-in-press-whiptail-lizards-and-hawaiian-trees/ Aspidoscelis inornata (male)

Nicholas G. Crawford, Jaime Zaldívar-Rae, Cris Hagen, Amanda Schable, Erica Bree Rosenblum, Jeff A. Graves, Tod W. Reeder, Michael G. Ritchie, Travis C. Glenn. 2007. Thirteen polymorphic microsatellite DNA loci from whiptails of the genus Aspidoscelis (Teiidae: Squamata) and related cnemidophorine lizards. Molecular Ecology Notes. In Press.

Metrosideros polymorpha

Nicholas G. Crawford, Cris Hagen, Heather F. Sahli, Elizabeth A. Stacy, Travis C. Glenn. 2007. Fifteen polymorphic microsatellite loci from Hawaii’s Metrosideros polymorpha (Myrtales: Myrtaceae), a model species for ecology and evolution. Molecular Ecology Notes. In Press.

]]> http://www.ngcrawford.com/2007/06/20/two-primer-notes-in-press-whiptail-lizards-and-hawaiian-trees/feed/ New Photo Sets http://www.ngcrawford.com/2007/04/13/new-photo-sets/ http://www.ngcrawford.com/2007/04/13/new-photo-sets/#comments Fri, 13 Apr 2007 16:07:24 +0000 Nick http://www.ngcrawford.com/2007/04/13/new-photo-sets/
]]> http://www.ngcrawford.com/2007/04/13/new-photo-sets/feed/ Excellent Scientific American Article with Answers to Creationist Arguements http://www.ngcrawford.com/2007/02/26/excellent-scientific-american-article-with-answers-to-creationist-arguements/ http://www.ngcrawford.com/2007/02/26/excellent-scientific-american-article-with-answers-to-creationist-arguements/#comments Mon, 26 Feb 2007 18:40:58 +0000 Nick http://www.ngcrawford.com/2007/02/26/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.

]]> http://www.ngcrawford.com/2007/02/26/excellent-scientific-american-article-with-answers-to-creationist-arguements/feed/ 2007 Bonnaroo Lineup http://www.ngcrawford.com/2007/02/14/2007-bonnaroo-artist-lineup/ http://www.ngcrawford.com/2007/02/14/2007-bonnaroo-artist-lineup/#comments Wed, 14 Feb 2007 16:05:06 +0000 Nick http://www.ngcrawford.com/2007/02/14/2007-bonnaroo-artist-lineup/ The PoliceSounds good! (um, no pun intended!)

The Police · Tool · Widespread Panic · The White Stripes · Ben Harper & the Innocent Criminals · Wilco · The Flaming Lips · Manu Chao · The String Cheese Incident · Franz Ferdinand · Bob Weir & Ratdog · Damien Rice · Ween · Gov’t Mule · Ziggy Marley · The Decemberists · Kings of Leon · Michael Franti & Spearhead · Wolfmother · Regina Spektor · The Black Keys · Galactic · DJ Shadow · Gillian Welch · Spoon · Keller Williams (WMD’s) · Sasha & John Digweed · STS9 · Old Crow Medicine Show · The Hold Steady · North Mississippi Allstars · Fountains Of Wayne · Hot Tuna · Feist · Hot Chip · John Butler Trio · Ralph Stanley & the Clinch Mountain Boys · Aesop Rock · The Richard Thompson Band · Dierks Bentley · Xavier Rudd · Gogol Bordello · Junior Brown · Tortoise · T-Bone Burnett · Mavis Staples · Clutch · Cold War Kids · Dr. Dog · Paolo Nutini · Brazilian Girls · RX Bandits · The Nightwatchman · The Slip · Girl Talk · Railroad Earth · Martha Wainwright · Rodrigo y Gabriela · Annuals · Tea Leaf Green · Sam Roberts Band · Elvis Perkins in Dearland · Charlie Louvin · Sonya Kitchell · Mute Math · Apollo Sunshine · Uncle Earl · James Blood Ulmer · The National · The Little Ones · Black Angels · Ryan Shaw

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