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Seth Russell magic-lantern

  • University of Colorado
  • Colorado
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@magic-lantern
magic-lantern / cust_mac.json
Created Apr 20, 2019
anne pro2 macos keyboard layout
View cust_mac.json
{"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"}
@magic-lantern
magic-lantern / sample_multiprocessing.py
Last active Apr 17, 2019
Small Python 3 script to show how to use multiprocessing for parallel processing of data
View sample_multiprocessing.py
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
@magic-lantern
magic-lantern / sample_future_lapply.R
Created Apr 2, 2019
Small R script to show how to use future.apply and future_lapply
View sample_future_lapply.R
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)
@magic-lantern
magic-lantern / ubuntu_r_upgrade_instructions.md
Last active Feb 1, 2019
Steps to upgrade Ubuntu 16.04 LTS from R 3.4.x to R 3.5.x
View ubuntu_r_upgrade_instructions.md

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):

@magic-lantern
magic-lantern / fhir_intro.md
Last active Nov 6, 2018
FHIR Introduction
View fhir_intro.md

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

@magic-lantern
magic-lantern / ngix-config
Last active Oct 26, 2018
Nginx Configuration for HTTPS RStudio Server reverse proxy
View ngix-config
##
# 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;
@magic-lantern
magic-lantern / eco.sh
Created Sep 13, 2018
Beta Environment Connection Script
View eco.sh
#!/bin/bash
read -p "Run 'ssh -q -D 1081 localhost' in a separate window (or before running this script). When running, press enter to continue.
"
# import the common commands
TOOLSDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null && pwd )"
source $TOOLSDIR/commands.sh
# grab the command line args
@magic-lantern
magic-lantern / proxy.pac
Last active Dec 13, 2018
Eureka Proxy.pac file for tunneling to App host
View proxy.pac
function FindProxyForURL(url, host) {
// the zotero service should only be local
if ( shExpMatch(url, "http://127.0.0.1:23119/*") ) {
return "DIRECT";
}
// localhost and google stuff should go to through socks proxy
if ((isPlainHostName(host) && shExpMatch(host, "localhost")) ||
(shExpMatch(url, "*127.0.0.1*")))
@magic-lantern
magic-lantern / eureka_notes.md
Last active Jun 3, 2019
Eureka Notes from beta testing
View eureka_notes.md

R Notes

RStudio Server General Setup

RStudio Server is installed and is the recommended method for using R in Eureka. It is also possible to use RStudio desktop version via VNC as well as the R commandline client.

Currently it doesn't seem possible to use your Eureka account with RStudio Server, so you have to create a new user on your Eureka server to use with RStudio Server. The password can be whatever you set - you may get warnings about password complexity, but any password will work. Creating a new user with some special settings allows for near seamless use between the new user and your existing Health Data Compass account.

WARNING Before running these steps, make sure you have a second connection opened to your app VM where you are logged in as root (sudo su -) to fix anything that may go wrong. If you mess something up, you may lose root access.

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