Thursday, December 30, 2010

t1.micro for the win

Stumbled across this from earlier in the month, I really should pay more attention!

Nuff said! By simply spinning up the Amazon EBS-Backed (64-bit) ami-74f0061d solved all issues I had with java, and size and scale from my previous other two posts:

both of which are now totally obsolete - nice one AWS ninjas! ;-)

[ec2-user@ip-10-117-53-202 ~]$ uname -a
Linux ip-10-117-53-202 #1 SMP Fri Oct 22 18:48:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux

[ec2-user@ip-10-117-53-202 ~]$ java -version
java version "1.6.0_20"
OpenJDK Runtime Environment (IcedTea6 1.9.1) (amazon-
OpenJDK 64-Bit Server VM (build 19.0-b06, mixed mode)

For the win!

Wednesday, December 29, 2010

heading down route 53, dynamic dns for short $

Been hacking about with route53 for a day or so to replace a dynamic dns service. So far so good. The HTTP/XML stuff is a bit tricky, is a great reference example, but needed something to be a bit more easy to script around. I was about to bust out some extreme perl XML::Twig parsing action, but the folks over @ boto already have the core part of this nailed! Plus they have some lovely extra stuff in there also for cli based cloud mngt:

Tuesday, December 21, 2010

about me?

So AOL just purchased yesterday, after much delay my invite finally came through, so it was clearly time to join this crazy bandwagon - much fun:

Saturday, December 18, 2010

wordle and pubmed fun

Courtesy of Kevin Karplus, an old friend in secondary structure prediction and many other areas of genomics analysis. Find time to read Kevin's Blog when you get a chance!

I just had much fun trying out on my meager set of publications, using this as an injection method:

Came out with a lovely picture to share. It does a really nice job!

visor: slideyouty windowy nifty thingy with simbl

Neato code for slide out terminal windows that follow you around! Michele put me on to this one, she has been going fairly hard core gangbusters on GNU Screen just recently. It is a lovely "hack" in the truest sense in that it extends the core functionality of a binary bundle, also put me on to SIMBLPlugins which are also fabulous! Here's what you need to get cracking:

You also need SIMBL (also an awesome way to hack bundles. You can get an installer from here:

Many more plugins are also available:


Once SIMBL is installed, (I needed a reboot to get mine to load) Then you can do this to install for everyone:
isrv: jcuff$ sudo cp -r ~/Downloads/Visor.bundle/ /Library/Application\ Support/SIMBL/Plugins/Visor.bundle

Restart terminal, and enjoy your new shiny visor goodness!

Thursday, December 9, 2010

/me waves @ clouds

Hurray, finally it is here! introducing-apache-wave.html

So time to go grab the code via "hg" (apt-get install mercurial: yeah I know yet another "superior" version control system!) from:

$ hg clone wave-protocol

...and then attempt to install this on our freebie amazon instance... Alas it totally failed to "ant build" on the m1.tinyResult was a classic "out of memory error" (Killed)! Now time to be rather brave and locate the operating system swap partition on EBS... Lord knows if this is going to cost actual real money - or work for that matter!

Wednesday, December 8, 2010

cookie monster

So had an interesting web scraping issue with systems behind a cookie based "paywall". Turns out you can quickly and simply extract a working cookie file from Chrome's sqlite3 database. There is a whole bunch of stuff scattered across the web that has bits and pieces of how to do this. There are, as with all things a million ways to do anything. So assume you have carefully auth'd to the site using Chrome, you can then go on to delve into the cookie database to use it with curl etc. later on.  There are also ways that you can embed UID/PASSWD inside curl/wget cmd lines. However, plain text on the CLI is always something that gives me the heebie jeebies ;-) Here's what I found (oh and cygwin on windows is totally awesome! Don't try and run windows without it ;-)) First up, the Chrome schema. You can find the database file in:

Sunday, December 5, 2010

swift DNA blastn, with a quick png picture ca. 2002 vintage

Sometimes even in 2010, you just really, really need to do things in a hurry. Like mapping a small set of reference sequences against a set of multiple DNA databases to prove existence or location - simple stuff. Then you also probably want to quickly draw a simple reference picture? Well back in the bad old days, this used to be a nightmare to do with any kind of velocity. Now with *much* faster CPUs, and way, way better code, it is fortunately trivial. However, you do have to remember that a considerable number of giants have gone before you; remember to always use their epic foo!

Here's an example from this year (2010) using some of the skills of (2002 vintage):

[any opinions here are all mine, and have absolutely nothing to do with my employer]
(c) 2011 James Cuff