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// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

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#!/usr/bin/env ruby

# WHAT WE DO HERE
# Take a link
# Add it as a bookmark

# Two inputs needed
if ARGV.count != 4
  abort "$0 username email password weblink"
end

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#!/usr/bin/env ruby

# Four inputs needed
if ARGV.count != 4
  abort "$0 username email password article-id"
end
username  = ARGV[0]
email     = ARGV[1]
password  = ARGV[2]
id        = ARGV[1]

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library(connectir)
library(boot)

# data = model
boot_mdmr <- function(formula, data, indices, sdist, factors2perm) {
    ###
    # Distances
    ###
    
    # We need to sample the distances based on the indices

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import sys
#sys.path.append("/Users/zarrar/Dropbox/Code/C-PAC/CPAC/cwas")
sys.path.insert(0, "/home2/data/Projects/CPAC_Regression_Test/2013-05-30_cwas/C-PAC/CPAC/cwas")
sys.path.append("/home/data/PublicProgram/epd-7.2-2-rh5-x86_64/lib/python2.7/site-packages")

import multiprocessing
import numpy as np
from mdmr import mdmr
from sklearn.metrics.pairwise import euclidean_distances

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import numpy as np
from CPAC.cwas.subdist import norm_cols
from fast_ecm import fast_eigenvector_centrality # this is from the other gist; can ignore this and paste in the other function

print 'Compare with non-normalized matrices'

m  = np.random.random((200,1000))
cm = m.T.dot(m)

# Let's first call a basic approach

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Packages

• lxml - Pythonic binding for the C libraries libxml2 and libxslt.
• boto - Python interface to Amazon Web Services
• Django - Django is a high-level Python Web framework that encourages rapid development and clean, pragmatic design.
• Fabric - Library and command-line tool for streamlining the use of SSH for application deployment or systems administration task.
• PyMongo - Tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
• Celery - Task queue to distribute work across threads or machines.
• pytz - pytz brings the Olson tz database into Python. This library allows accurate and cross platform timezone calculations using Python 2.4 or higher.

Guides

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Gems

• Bundler - Bundler maintains a consistent environment for ruby applications. It tracks an application's code and the rubygems it needs to run, so that an application will always have the exact gems (and versions) that it needs to run.
• rabl - General ruby templating with json, bson, xml, plist and msgpack support
• Thin - Very fast and lightweight Ruby web server
• Unicorn - Unicorn is an HTTP server for Rack applications designed to only serve fast clients on low-latency, high-bandwidth connections and take advantage of features in Unix/Unix-like kernels.
• SimpleCov - SimpleCov is a code coverage analysis tool for Ruby 1.9.
• Zeus - Zeus preloads your Rails app so that your normal development tasks such as console, server, generate, and specs/tests take less than one second.
• [factory_girl](h

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import numpy as np
import os
#from CPAC.network_centrality import load
#from CPAC.cwas.subdist import norm_cols

import nibabel as nib
from scipy.sparse import coo_matrix, cs_graph_components

def load(datafile, template):
    

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#!/usr/bin/env python

import argparse
import os
from os import path

from CPAC.network_centrality import calc_centrality


###