michaelbarton

require 'open-uri'
require 'rubygems'
require 'hpricot'

ARGV.each do |gi|

  # Fetch the URL and pass the contents to Hpricot
  url = "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=#{gi}&rettype=fasta&retmode=xml"
  doc = Hpricot.XML(open(url).read)
 

michaelbarton

library(reshape)
library(lattice)

#
# Categorical example
#

data1 <- read.csv(file="plots/categorical.csv")

# Reshape the data into long format

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# Prompt with just directory basename
PS1="\W $ "

# Colourise ls output an sort by size
alias ls='ls -l -G -t'

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  desc 'Loads all the alignment codon data'
  task :load_alignment_codons => :clear_alignment_codons do
    starfish = %x|which starfish|.strip
    loader = PROJECT_ROOT + '/model/starfish/load_alignment_codons.rb'
    p = lambda{ system( "qsub -cwd -j y -V #{starfish} #{loader}") }

    p.call
    sleep(120)
    16.times { p.call }
  end

michaelbarton

Task: Blast
  Run BLAST
  Using the protein sequence for YDL177C
  On uniprot
  Return all hits with e < 0.00001

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BLAST protein YDL177C
BLAST dna YDL177C

michaelbarton

# Given the location of an SQL query file, this method will
# execute the query on the database, and print each line to 
# the supplied target file.
# This method relies on the MySQL adapter for the fetch_fields 
# method, but should not suffer in performance from pulling 
# large amounts of data into memory.

public

def export_csv_from_sql(sql_file,target_file)

michaelbarton

# Example activerecord interator based on using an indexed 'id' column.
# See http://schuerig.de/michael/blog/index.php/2007/02/03/ar-enumerable/
# and http://weblog.jamisbuck.org/2007/4/6/faking-cursors-in-activerecord

class << ActiveRecord::Base
  def each(chunk_size=1000)
    (0..self.last.id / chunk_size).each do |offset|
      self.find(:all,
        :limit => chunk_size,
        :conditions => ["id > ?", offset * chunk_size]).each do |i|

michaelbarton

require 'fileutils'
require 'find'

class Latex < Thor

  desc "build","builds thesis document"
  method_options :src  => 'src',
                 :dest => 'out',
                 :tmp  => 'tmp'
  def build(file)

michaelbarton

- Example where
  - cost of alanine is being considered
  - in glucose limitation
  - at biomass flux of 0.5

- Set all exchange fluxes to have a lower bound of -10000.
  - Effectively unlimited nutrients with respect to biomass flux

- Set biomass flux reaction rate to have upper and lower bounds of 0.05