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# bash colours
export CLICOLOR=1
export LSCOLORS=GxFxCxDxBxegedabagaced

# define colors
C_DEFAULT="\[\033[m\]"
C_WHITE="\[\033[1m\]"
C_BLACK="\[\033[30m\]"
C_RED="\[\033[31m\]"
C_GREEN="\[\033[32m\]"

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Open science & data

• Panton Fellowship from the OKFN - funds individuals for one year to support promotion of openness.
• Center for Open Science grants - funds for projects (e.g. open source software) that promote or enable good open scientific practices. [via @rmounce]
• Alfred P. Sloan Foundation Digital Information Tech grants - funds for projects to support:
  • data-intensive science
  • utilisation of open data
  • digitising and enabling access to knowledge [via @rmounce]

Scientific software best practise

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if ("devtools" %in% loadedNamespaces()) {
  stop("You must restart R before installing devtools")
}

url <- "https://github.com/hadley/devtools/archive/v1.4.1.zip"
temp <- file.path(tempdir(), "devtools.zip")

setInternet2(TRUE)
suppressWarnings(download.file(url, temp, mode = "wb"))
install.packages(temp, repos = NULL)

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# convert transcript ID to gene ID
df <- data.frame(a = c("AT1G2.1", "AT1G2.3", "AT1G2.3", "AT1G3.1", "AT1G3.3", "AT1G3.3"), b=1:6)
df$t <- gsub(df$a, pattern="\\.[0-9]+", replacement="")

# sum by gene ID
aggregate(df[,2], by=list(as.factor(df$t)), sum)

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List of software to be pre-installed on VMs for SeqAhead course.

Transcriptome optimisation

• RVM with latest Ruby (http://rvm.io/ - to install: \curl -sSL https://get.rvm.io | bash -s stable --ruby).
• BLAST+ (latest version)
• Bowtie2 (latest version)
• CD-HIT (http://www.bioinformatics.org/project/filelist.php?group_id=350)
• eXpress 1.5.1 (http://bio.math.berkeley.edu/eXpress/overview.html)
• SoapDenovoTrans, fixed version from GitHub (https://github.com/cboursnell/SOAPdenovo-Trans)

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#! /udr/bin/env ruby

require 'twitter'
require 'rmagick'
require 'open-uri'

# set up the twitter client
client = Twitter::REST::Client.new do |config|
  config.consumer_key        = # redacted
  config.consumer_secret     = # redacted

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#!/usr/bin/env ruby

require 'bio'
require 'inline'
require 'benchmark'
require 'trollop'


class TestC

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# This is the default configuration file. Enabling and disabling is configured
# in separate files. This file adds all other parameters apart from Enabled.

inherit_from:
  - enabled.yml
  - disabled.yml

# Common configuration.
AllCops:
  # Include gemspec and Rakefile

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 class Combinator

  include Enumerable
 
  def initialize parameters
    @parameters = parameters
  end
 
  def generate_combinations(index, opts, &block)
    if index == @parameters.length

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#! /usr/bin/exec node

var Spooky = require('spooky');
var dom = require('jsdom').jsdom;
var xpath = require('jsdom-xpath');

// Set up the spooky agent to retrieve URLs
var spooky = new Spooky({
  child: {
    transport: 'http'