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# Test of docker build process
#
# ctd - Crash Test Dummy. "You can learn a lot from a dummy"
#
# Sample commnds
# date; docker build --tag ctd:1.0 .; date
# docker history ctd:1.0
# docker run -i -t ctd:1.0 /bin/bash
# this whole thing should take 30 - 35 minutes on first run
FROM rocker/r-ver:3.6.3

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Eureka GPU Setup Guide

Git

CentOS 7.6.1810 has a very old version of Git (v 1.8.3.1 from ~ 2013). To install a current version of Git, you have a few options:

From Source

sudo yum -y install wget perl-CPAN gettext-devel perl-devel openssl-devel zlib-devel

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{"name":"SethMac","device":1,"model":3,"type":"layout","data":{"layer0":[41,30,31,32,33,34,35,36,37,38,39,45,46,42,43,20,26,8,21,23,28,24,12,18,19,47,48,49,57,4,22,7,9,10,11,13,14,15,51,52,40,225,29,27,6,25,5,17,16,54,55,56,229,224,226,227,44,231,192,193,228],"layer1":[53,58,59,60,61,62,63,64,65,66,67,68,69,76,0,0,82,0,0,0,0,0,82,0,70,74,77,0,0,80,81,79,0,0,0,80,81,79,75,78,0,0,0,0,0,0,0,0,0,0,73,76,0,0,0,0,0,0,192,193,0],"layer2":[53,200,201,202,203,0,170,169,168,241,240,244,243,76,0,0,82,0,0,0,0,0,82,0,70,74,77,0,0,80,81,79,0,0,0,80,81,79,75,78,0,0,0,0,0,0,0,0,0,0,73,76,0,0,0,0,0,0,192,193,0],"taps":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,53,0,0,0,0,0,0,0,0,0,0,82,0,0,0,0,0,80,81,79]},"crc":"da16ca4b"}

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import pandas as pd
import numpy as np
import multiprocessing
from multiprocessing import Pool

num_processes = multiprocessing.cpu_count()
# on some systems, these next 2 lines will give better count for CPU intensive tasks
# import psutil
# num_processes = psutil.cpu_count(logical=False)
num_partitions =   num_processes * 2 #smaller batches to get more frequent status updates

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library(future.apply)

# set parallel_processing to TRUE if parallelization desired
parallel_processing <- TRUE
num_workers <- availableCores() # this option will automatically scale to fit current machine

# default plan for future.apply/future is sequential (no parallelization)
# plan(multiprocess) should pick recommended option based on OS
if (parallel_processing) {
  plan(multiprocess, workers = num_workers)

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Steps to upgrade r:

From linux command-line remove all existing R packages:

sudo apt-get update
sudo apt-get remove r-base r-base-dev r-base-core r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart  r-cran-spatial r-cran-survival r-doc-html r-recommended

Next, update /etc/apt/sources.list and add these lines (comment out old R version, add new pkg list):

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Introduction

Fast Healthcare Interoperability Resources (http://hl7.org/fhir) - FHIR – is a standards framework created by Health Level 7 (HL7). FHIR combines the features of HL7's previous health data interchange standards including HL7 v2 , HL7 v3 and CDA. FHIR improves on previous standards by using more modern web standards for data exchange, supports many programming languages, and promostes human readability.

Documentation

Start by reading through this first: "FHIR Drills" https://fhir-drills.github.io/index.html

• Python Client: http://docs.smarthealthit.org/client-py/
• Java Client: http://hapifhir.io/doc_rest_client.html

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##
# Customized Nginx configuration
##

server {
        root /var/www/html;
        index index.html index.htm index.nginx-debian.html;
        server_name rstudio.learnclinicaldatascience.org; # managed by Certbot

        access_log            /var/log/nginx/rstudio.learnclinicaldatascience.org;

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function FindProxyForURL(url, host) {

    // the zotero service should only be local
    if ( shExpMatch(url, "http://127.0.0.1:23119/*") ) {
        return "DIRECT";
    }

    // localhost and local stuff should go to through socks proxy
    if (shExpMatch(host, "skylark.ucdenver.pvt") ||
        shExpMatch(host, "rainier.ucdenver.pvt") ||