Analysing Data on Armis or Great Lakes using Rmd Files
From Bridges Lab Protocols
Contents
Software
On OSX
- Install Filezilla for file transfers https://filezilla-project.org/
On Windows
- Install Putty for command line access https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html
Access
At Michigan there are two clusters, one for human data (Armis) and one for non-PHI data (Great Lakes). Both of these are connected to a storage service called Turbo. These are available as part of the UM Research Computing Package.
Permissions
- For access to https://datadirect.precisionhealth.umich.edu/, you need to complete these two online classes and have the VPN installed on your device. For more details on access follow these instructions.
- PEERS - Human Subjects Research Protections
- HIPAA Training for Self Service Tools.
- You also need an approved IRB noting that you will use the data direct self-service tools.
- To get access to Armis2 fill out this form.
You can access the server either through the command line or through a remote desktop if you prefer a GUI. There a limited functionality to Armis2 here that can also be used (see these instructions).
If you submit a deidentified data request via https://datadirect.precisionhealth.umich.edu, your data will be sent as a 7zip file to the turbo storage in a folder named for your IRB. You will be prompted to enter a password to protect this file.
