This textbook was written for the clinical research community at Johns Hopkins leveraging the precision medicine analytics platform (PMAP). These notebooks are available in html form on the Precision Medicine portal as well as in computational form in the CAMP-share folder on Crunchr (Crunchr.pm.jh.edu).

• Platform Tool : Jupyter/Crunchr on PMAP using
• Programming Language :
• Author(s) : Paul Nagy
• License : The notebook is released under the Apache 2.0 License
• Last Updated : May 28th, 2019

Crunchr

Table of Contents

• What is Crunchr
• How to get to Crunchr
• How to get to the PMAPCookbook

Crunchr

Crunchr is a web-based collaborative data science platform built on PMAP allows Clinical researchers to

• to share file systems with a research team
• gain access to data via database and file based systems in PMAP
• create and share Jupyter notebooks to perform analysis
• create containers and install custom libraries

Crunchr was built on the open source SciServer. SciServer was written by the Institute for Data Intensive Engineering and Science at Johns Hopkins University with the goal of building "A collaborative research environment for large-scale data-driven science". SciServer is funded by the National Science Foundation through its Data Infrastructure Building Blocks (DIBBs) program.

How to get to Crunchr

Step One. Launch SAFE

For security purposes, Crunchr platform can only be reached from the Safe Desktop.

Step Two. Launch Chrome in SAFE

When in the desktop launch the Chrome browser

Step Three. Goto Crunchr website

From the browser go to https://crunchr.pm.jh.edu

How to access the PMAP Cookbook on Crunchr

Step One. Goto Compute box in Crunchr

On the main Crunchr page, click on the compute area.

Step Two. Create a new container

Now you are going to create a docker container that will setup an environment to compile jupyter notebooks. here is the container management screen. You are allowed to have up to 3 containers. Click on create new container.

Step Three. Ensure container has getting-started user volume

Now you need to setup a new container. You can name the container anything you like (here i have named it Cookbook. Make sure to select the getting-started volume which will allow you access to the cookbook notebooks. Then click on the Create button.

You should now see a new container with the name you selected. Click on the name of the container to launch it in a new window.

Step Four. Click on new container to open

Step Five. Click on getting-started folder

Congratulations. You are now in Jupyter. Jupyter can serve as a file explorer. Click on the getting-started folder.

Step Six. Click on the PMAPCookbook folder.

Step Seven. Click on the 0_Start_Here.ipynb

You are now in the folder with several notebooks. Click on the 0_Start_Here.ipynb to launch the main table of contents for the text books.

Welcome to the PMAP Cookbook. These are a collection of Jupyter notebooks to help you explore how to conduct research on clinical data.

Note: While you can load and run notebooks, you cannot save anything in this directory. This directory is read only. You will need to save a copy of the files to your directory and run them their.