neilfws

gse <- getGEO("GSE45016") # you want GSEMatrix = TRUE

# ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/
# Found 1 file(s)
# GSE45016_series_matrix.txt.gz
# trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE45nnn/GSE45016/matrix/GSE45016_series_matrix.txt.gz'
# ftp data connection made, file length 1486394 bytes
# opened URL
# ==================================================
# downloaded 1.4 Mb

neilfws

#!/usr/bin/ruby
# save as pubmed.rb and test using 'ruby pubmed.rb 19662644'
# keyword search may return > 1 record due to retmax bug
# http://github.com/bioruby/bioruby/commit/51c3223e033b2992a7bd95da282f88164406ff92

require 'rubygems'
require 'bio'

keywords = ARGV.join(' ')

neilfws

require 'open-uri'
require 'json'
require 'mongo'

class FriendFeed
  attr_accessor :user, :database, :collection
  
  def initialize(user, database, collection)
    @user = user
    @database = XGen::Mongo::Driver::Mongo.new.db(database)

neilfws

# mongodb.rake for Rails
# assumes that mongodb installed in Rails.root/lib/mongodb

namespace :db do
  namespace :mongo do

    # start db server
    task :start do
      pr = get_pids
      if pr.length == 0

neilfws

#!/usr/bin/ruby

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

doc = Hpricot(open("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=gds"))

(doc/'//fieldlist/field').each do |f|
  puts "#{(f/'/name').inner_html},#{(f/'/fullname').inner_html},#{(f/'description').inner_html}"

neilfws

namespace :db do
  require "mongo"
  require "json/pure"
  require "open-uri"

  feed    = ENV['feed']
  db      = Mongo::Connection.new.db('friendfeed')
  col     = db.collection('entries')

  desc "Seed database with feed entries"

neilfws

# install GEOmetadb
source("http://bioconductor.org/biocLite.R")
biocLite("GEOmetadb")
library(GEOmetadb)

# connect to database
getSQLiteFile()
con <- dbConnect(SQLite(), "GEOmetadb.sqlite")

# count samples per GDS

neilfws

#! /bin/sh

### BEGIN INIT INFO
# Provides:          mongodb
# Required-Start:    $all
# Required-Stop:     $all
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: starts the mongodb data-store
# Description:       starts mongodb using start-stop-daemon

neilfws

#!/usr/bin/env ruby
require 'rubygems'
require 'daemons'
dir = File.expand_path(File.join(File.dirname(__FILE__), '..'))

daemon_options = {
  :multiple   => false,
  :dir_mode   => :normal,
  :dir        => File.join(dir, 'tmp', 'pids'),
  :backtrace  => true

neilfws

sau103@gymea-nh:~$ ruby -v
ruby 1.8.7 (2009-06-12 patchlevel 174) [i486-linux]

sau103@gymea-nh:~$ boson -hv
boson [GLOBAL OPTIONS] [COMMAND] [ARGS] [COMMAND OPTIONS]

GLOBAL OPTIONS
+-------------------+-------+---------+-------------------------------------------------------------------+------------------+
| Name              | Alias | Type    | Desc                                                              | Values           |
+-------------------+-------+---------+-------------------------------------------------------------------+------------------+