mndoci

require 'rubygems'
require_gem 'activerecord'
require '/var/www/hoosier/app/models/payment_method'

#Connect to the database
ActiveRecord::Base.establish_connection(
    :adapter  => "postgresql",
    :host     => "localhost",
    :username => "****",
    :password => "****",

mndoci

Task: Protein lookup
  Find protein structure for 1MBN
  From PDB
  Return sequence of protein

Task: Blast
  Run BLAST
  Using the protein sequence from Protein lookup task
  On uniprot
  Select all hits with e < 0.00001

mndoci

# This is a simple command line tool for uploading
# and folders of files to AWS S3. You must first
# create a vaild bucket to upload to.

#!/usr/bin/env ruby
require 'rubygems'
require 'pathname'
require 'aws/s3'

include AWS::S3

mndoci

#!/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
# From Neil Saunders http://gist.github.com/164994

require 'rubygems'
require 'bio'

keywords = ARGV.join(' ')

mndoci

# If you use osx terminal/git this includes a couple nice features:
#   1) Minimalist colors
#   2) Stripped down CLEAN prompt
#   3) For GIT folders it will display the current branch.
# To install just copy this into the top of your ~/.bash_profile
# Based on http://www.simplisticcomplexity.com/2008/03/13/show-your-git-branch-name-in-your-prompt/

function parse_git_branch {
  git branch --no-color 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/[\1]/'
}

mndoci

#SWITCHES
#-d (cap deploy when check-in finished)
#-v (verbose, defaults to quiet)
#-m "commit message" (custom commit message)

#!/bin/bash
## options to be accepted
optstr=m:dv ## colon follows options that require an argument
while getopts $optstr var
do

mndoci

      === Epic Snow Leopard Upgrayyyyd Guide ===

Son, you’re now living in the land of 64-bit systems.

That means that some of your 32-bit shit is now broken.

Not all is lost.

== Fixing MySQL weirdness

mndoci

#!/bin/sh
# -*- sh -*-

export JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Home
export PATH=$JAVA_HOME/bin:$PATH

CLJ=$HOME/Projects/clj/clojure

java \
    -server \

mndoci

(ns examples.fs
(:import
  (org.apache.log4j Level Logger)
  (java.io BufferedReader InputStream InputStreamReader))

(:use [clojure.contrib.test-is :only (deftest is)])
(:use [clojure.contrib.except :only (throwf throw-arg)])

(:require [clojure.contrib.duck-streams :as ds]
          [examples.imports :as import]))

mndoci

(ns examples.fs
(:import
  (org.apache.log4j Level Logger)
  (java.io BufferedReader InputStream InputStreamReader))

(:use [clojure.contrib.test-is :only (deftest is)])
(:use [clojure.contrib.except :only (throwf throw-arg)])

(:require [clojure.contrib.duck-streams :as ds]
          [examples.imports :as import]))