gawbul

#!/usr/bin/ruby
require 'sqlite3'

cite_part = ARGV[0]
db_name = "/Users/nernst/Library/Application\ Support/Mendeley\ Desktop/neil\@neilernst.net\@www.mendeley.com.sqlite"
db = SQLite3::Database.new( db_name )
db.results_as_hash = true
query = "select citationkey, title, year from Documents where citationkey like '%#{cite_part}%'"#MATCH '#{cite_part}'"#{}like '%#{cite_part}%'"
db.execute( query ) do |row|
  print row['citationKey'] + '|'

gawbul

#!/usr/bin/python
'''
Launch codeml on all the alignments

Marco Galardini 2012
University of Florence
GPL v3.0
'''
from optparse import OptionParser, OptionGroup
from time import strftime

gawbul

GNU GENERAL PUBLIC LICENSE

Version 3, 29 June 2007

Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/>

Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

gawbul

What

Roll your own iPython Notebook server with Amazon Web Services (EC2) using their Free Tier.

What are we using? What do you need?

• An active AWS account. First time sign-ups are eligible for the free tier for a year
• One Micro Tier EC2 Instance
• With AWS we will use the stock Ubuntu Server AMI and customize it.
• Anaconda for Python.
• Coffee/Beer/Time

gawbul

gawbul

-----BEGIN PGP PUBLIC KEY BLOCK-----
Version: GnuPG/MacGPG2 v2.0.27
Comment: GPGTools - https://gpgtools.org

mQINBFUATqwBEAD5zjucZ/orZU5KLqLpVhqUyV0m3+ELVu3hNJL05X4d8go3ynWQ
6kYq2vtD9g+illHMQubA41k5/KhCWx/E/v33JpMbvr6EDuqlwZ6SUjp+k8KZ4Gja
UZu3cm2dx9JnvTvnDPb7vB16m/tbF01N22JhBu/AeX5Qv7+MesJ1gZtyC20p1iDf
660yd/wFPSiXAoCOq2inbC/quKH/1DJQbsknBmJDHR4GuMR6rybCr0GEqBUGws65
0Pj3olC8cSG6WM7OlZ9rXW57vwZeoSLWCoQoShRPFjzu3tHYPM+LTGxcs40cNydN
VluZgi7/0FpNi60JraidV5UYOUkpxTEbqgRtObACJV45K4xLQmS/CgrL5DS9HMS2

gawbul

{
 "metadata": {
  "name": "Microarray Heatmap in R"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {

gawbul

@@ ENSFM00500000274301	(((((((((Homosapiens<1>_0.010967:6.4,Pantroglodytes<1>_0.004562:6.4)_0.007859:2.4,Gorillagorilla<1>_0.012414:8.8)_0.005772:6.9,Pongoabelii<1>_0.004608:15.7)_0.004809:4.7,Nomascusleucogenys<1>_0.004848:20.4)_0.005138:8.8,Macacamulatta<1>_0.004726:29.2)_0.006389:13.4,Callithrixjacchus<1>_0.004113:42.6)_0.005382:22.6,Tarsiussyrichta<0>_0.012865:65.2)_0.006876:8.8,(Microcebusmurinus<1>_0.003875:57.9,Otolemurgarnettii<1>_0.002941:57.9)_0.001924:16.1)_0.005017:16,Tupaiabelangeri<1>_0.000000:90)
@@ ENSFM00500000274300	(((((((((Homosapiens<1>_0.004779:6.4,Pantroglodytes<1>_0.005284:6.4)_0.006865:2.4,Gorillagorilla<1>_0.005655:8.8)_0.004013:6.9,Pongoabelii<1>_0.004926:15.7)_0.006409:4.7,Nomascusleucogenys<0>_0.010497:20.4)_0.001390:8.8,Macacamulatta<2>_0.009068:29.2)_0.004651:13.4,Callithrixjacchus<1>_0.005251:42.6)_0.004780:22.6,Tarsiussyrichta<0>_0.008096:65.2)_0.002459:8.8,(Microcebusmurinus<1>_0.005100:57.9,Otolemurgarnettii<1>_0.001525:57.9)_0.009555:16.1)_0.008878:16,Tupaiabelangeri<1>_0.0

gawbul

BEGIN {
  FS="\t"
}
{
	lena=split($9,a,",")
	for (i=1;i<=lena;i++) {
		split(a[i],b,"_")
		freq[NR][b[1]]++
	}
}

gawbul