Using the Silo Environment

Silo is the SSCC's secure computing enclave. It consists of secure servers and data storage for working with data covered by HIPAA and other sensitive data. Currently, the Silo servers are all Windows-based and very similar to Winstat. New Linux servers will be available very soon.

Getting Access

If you are interested in using Silo, please contact the SSCC Help Desk. Depending on the nature of your data you may still need to get explicit approval from your IRB, the UW-Madison Office of Cybersecurity, or other relevant authorities before you can store data in Silo, but using Silo will expedite that process because it has already been approved for other projects.

Connecting to Silo requires multifactor authentication using Duo, the same system used for your UW-Madison NetID. Most people use the Duo app on their smartphone, but you can also use a separate hardware token. When you contact the Help Desk about using Silo please mention which method you prefer. Instructions for obtaining and using a hardware token can be found here.

Installing the Citrix Workspace App

To use Silo you'll need to have the Citrix Workspace App installed on your computer. Just click on the appropriate link below and then run the installer after it finishes downloading. If you've already installed the Citrix Workspace App on your computer in order to use Winstat you do not need to install it again.

See Using Winstat for more information about using the Citrix Workspace App.

Logging In

To log in to Silo, you will need go to the web site If you're asked to give permission for programs to run, do so.

silo login screen

At the login screen, first give your SSCC username and password as usual. If it is your first time logging into Silo, you'll be prompted to follow the instructions on the screen to set up Duo on your smartphone. You'll be able to use the same Duo app for both Silo and your NetID.

The Silo File System

Silo uses a Linux-based file system. It is separate from the SSCC's main Linux file system, but we've given the drives the same names. Thus Z: is your home directory on Silo, and project folders are found on V:. Most research data will go in project folders, as home directories are initially limited to 20GB and expanded to 40GB on request.

Moving Files To and From Silo

Silo has its own file system and the ability to move files to and from that file system is intentionally limited.

To move sensitive data to Silo, contact the SSCC Help Desk and we'll work with you to find the most convenient way to transfer your data.

To move public data, program files, or other files to Silo, put them in a folder on your Z: drive in the regular SSCC file system and then contact the SSCC Help Desk and ask that that folder be copied to Silo.

Moving data off of Silo's file system is simpler. We have created a folder called silosync in the Z: drive of each Silo user. Every five minutes, an automated script copies anything placed in this folder to a corresponding folder in the user's Z: drive on the SSCC's primary file system. Similar folders can be created within project folders. Files are not copied from the main SSCC file system to Silo. It is your responsibility to ensure any data you place in the silosync folder can be appropriately stored on the SSCC's main file system and do not require the additional security Silo provides.

Using Silo

Once you've logged in, Silo behaves just like a regular Winstat server, with a few important exceptions:

  • Silo cannot access the Internet. This can affect programs in unexpected ways: for example, Stata's findit command takes much longer to run than usual and then only gives partial results, because it tries to reach Stata's web server and does not display any results until that attempt times out. Fortunately the results it does give are the ones you're most likely to need.
  • You can install R packages from CRAN and Bioconductor, Stata packages from SSC, and Python packages from PyPI. If you need to install packages from other sources contact the Help Desk.
  • You cannot copy and paste between Silo and your own computer.
  • Silo cannot access disk space on your computer.
  • You cannot print from Silo.

Silo Downtime

Silo has a downtime from 7:00am-9:00am the first Wednesday of the month for security updates.  

Logging in Using a Hardware Token

If you would like to use a token to log into Silo and have one already, please contact the Help Desk and include the serial number printed on the back of your token in your email. The token must be black and white colored, with the words "OTP c100" printed on the front - we cannot use the blue and green tokens that say "Duo" on the front. If you do not have a token, please let us know and we will issue you one.

Silo token types

Log in by going to and giving your SSCC username and password as usual. Then click Enter a Passcode and press the button on your token. Enter the 6-digit number from your token and click Log In.

If later you wish to add a smartphone app to your Silo account so you can authenticate with either the app or a token, click Add a new device under the SSCC logo and follow the onscreen instructions.

If you have any questions about using Silo, feel free to contact the Help Desk.

Last Revised: 3/19/2020