Nick’s Blog

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.

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.

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!

[youtube:http://www.youtube.com/watch?v=GL7uW4TYqbs]

[youtube:http://www.youtube.com/watch?v=xR8MGAsidFI]

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.

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.

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.

Sounds 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

This is pretty funny. Well, if you surf the net as much as I do that is!

So there is actually a part two or maybe more accurately a corollary story to my original “Crazy Southern Rednecks” email. Yup, there is a whole other tale I did not reveal in the first note. Here is how it goes…

Remember how I was on the phone with my friend Chris when the good ol’ boy pulled the gun? Well, as soon I told Chris what was going on he said something like,

“Oh yeah, he pulled one on Lesley last week!”
“Lesley?” I asked.
“Kimberley’s friend, you haven’t met her…. Do you have a pad and a pen?”
“Like something to write on?”
“Yeah, Lesley said he was a deaf mute!”

As I was not planning on talking to banjo boy all grown up, I did not feel this advice applied to me. Anyway, once I got to Chris’s house I heard the rest of the story.

Essentially, Kimberley’s friend Lesley came to visit the week before and made the same wrong turn down the same dingy drive way that I did. However, she was not as lucky as myself and the guy blocked her in before she could leave. According to Chris she was not sure if he threatened her with gun as his hand was hidden, but she did indicate that he required a pen and pencil to communicate. She said he scrawled something like ‘what yah doin?’ and she wrote back ‘I’m lost.’ Apparently he was belligerent and would not let her leave for 45 minutes.

I have not actually met Lesley yet so the authenticity of this story is perhaps a bit in doubt. However, I will do my best to interview the girl and report back.