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

Steps to using Crunchr for collaborative research

Table of Contents

• Collaborative research
• Creating a shared user volume
• Creating a group
• Starting a compute container
• Getting technical support

Collaborative Research

The Crunchr system is a website built for collaborative research allowing the sharing of computational notebooks with research teams. There are three steps to follow.

1. Create a shared User Volume to share notebooks with your team.
2. Add your team to have access to that folder through Group priveleges.
3. Launch a container for analysis that attaches to that User Volume.

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

By launching this browser from SAFE, you will login automatically to Crunchr and should see your JHED account ID in the upper right and corner.

*Note: Compute containers and Jupyter notebooks will expire after 24 hours. Please close browser tabs and reload the Crunchr home page to reset your session.

1. Creating a shared user volume

In this step you want to create a folder to share with your research collaborators. As the creater of the folder, it will be created under your JHED directory, but others will be able to access it.

Creating a new User Volume can be done from the File management page. You can also see all of your shared folders from this view.

Creating a new volume should be done in the persistent storage folder.

Once created, you will see it in your File management page.

2. Creating a group

From the home landing page of Crunchr, click on the groups link.

The Groups section allows you to

1. Create a new group
2. Assign a group to a User Volume
3. Add/Edit a users rights (Admin/user)
4. Edit a groups right to a User Volume (Read/Write)

To create a new test group from the Groups page click on the plus button highlighted below.

Name the group around the research project

Now you can go to middle window and select which user mounts you want to provide this group access to

Here you can set the degree of control the users of the group can have from Read only. Read/Write should be sufficient for most research projects.

Now you can click on the right members window to add members to this group.

You can select members by typing in their JHED ID. The system will perform autocompletion to help you select a valid JHED>

Note: If you don't see the person's JHED ID. Ensure they have logged into Crunchr at least once. This step auto provisions their account and will allow you then to be able to add them to your group.

You now need to select the Invite button to send them a notification inviting them to your group. You will be asked whether you want to make them a regular member or an Admin with the ability to add/remove users on their own.

You should now see them as a member of your group. Their status will change from Invited to Member when they accept the invitation.

Starting a compute container

A container is the environment you specify the software libraries specific to the analysis you are performing. Click on the green Create Container button.

PMAP Comes with a default container that is designed for data science analysis. You can customize the container for your specific applications in the environment. Users can create up to 3 containers at one time.

Note: Be sure to select the relevant User Volumes for the project you are working on.

Once the container has been constructed for you, click on the hyperlink name of the container you just created to launch it.

This will launch you into the Jupyter environment. Jupyter is a powerful open source research environment. Learn more about Juptyer

One of the functions Jupyter provides is as a file explorer.

To get to shared volume the User Volume click on the Storage directory.

And then click on the JHED ID of the person who created the User Volume. Only User Volumes are visibile to invited research collaborators. In this example we named it Project123.

Congratulations, now you have a shared workspace to access and analyze data.

Getting technical support

On the home page of PMAP you should see your userid. By right clicking on your user ID you will see a pulldown option labeled 'Ask for help'. Click there

That will take you to our issue submission form. The PMAP system is a research system and is support by the Johns Hopkins Information Technology group. The support for PMAP is not a mission critical clincial system, and provided from 9 to 5 on workdays.

here is a direct link