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gawbul / query_cite.rb
Created July 4, 2011 18:35 — forked from neilernst/query_cite.rb
Find citation keys using Mendeley
#!/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'] + '|'
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gawbul / parallelPAML.py
Created October 5, 2012 16:08 — forked from mgalardini/parallelPAML.py
Parallel Evolutionary Biology
#!/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
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gawbul / GPL.md
Created January 14, 2013 18:22 — forked from jnrbsn/GPL.md
GNU GPLv3 in Markdown

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
gawbul / roll_ipython_in_aws.md
Created March 31, 2013 20:39 — forked from iamatypeofwalrus/roll_ipython_in_aws.md
Roll your own IPython Notebook Server with AWS

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 / Microbial_Phylogenetics.ipynb
Last active December 19, 2015 12:38
Microbial Comparative Phylogenetics
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gawbul / steves_pgp_pubkey
Last active December 21, 2015 03:48
My GnuPGP Public Key
-----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
gawbul / gist:6400801
Created August 31, 2013 21:40
Microarray Heatmaps in R
{
"metadata": {
"name": "Microarray Heatmap in R"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
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gawbul / primates_varied_indiv.lambda
Created October 23, 2013 13:53
primates_varied_indiv.lambda
This file has been truncated, but you can view the full file.
@@ 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
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gawbul / parse_rad_tags.awk
Created December 9, 2013 22:33
A script to parse a RAD tags file and display the line number and individual id/tag id pairs field when the field has only a specific number of individuals (in the case n==3)
BEGIN {
FS="\t"
}
{
lena=split($9,a,",")
for (i=1;i<=lena;i++) {
split(a[i],b,"_")
freq[NR][b[1]]++
}
}
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gawbul / introduction_to_loops_for_biologists.ipynb
Last active January 4, 2016 05:39
Introduction to loops for biologists
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