Biotechnology Center


Data Transfer Instructions

Overview

UWBC provides multiple options to download deliverable data:
  1. The UWBC Facility Files download page is available to all UWBC clients. It provides good performance and an easy to use interface for downloading your data. If you download multiple files at once the page will create a zip archive. If you primarily download smaller files (Sanger sequencing, mass spec, etc.) this may still be the most convenient option since you don't need any special client software. For large or frequent downloads UW-Madison clients should consider the other options. Work is underway to provide additional downloading options for external clients.
  2. BRC account holders can connect to brchome.biotech.wisc.edu via SSH or SFTP to access their home directories.
  3. SFTP access is available to all UW-Madison clients with a UW NetID. Performance is slightly better than the web portal. The main advantages over the web portal are the capability to download multiple files without creating a zip archive and accessibility through command-line clients. Details are below on this page.
  4. Globus Connect is another option for UW-Madison clients with a UW NetID. This option provides the best performance, better than SFTP or the web portal. It also provides the best user experience, with email notifications of your download status and automatic retries of failed transfers. The initial server is limited to UW-Madison clients but work is in progress to make Globus Connect available to external clients as well. Details are below on this page.
Data access for deliverable data is based on your lab membership. Download directories are created for each PI. The PI, plus every member of the PI's lab who is set up in our system will have access to those directories.

Web Portal download:

Your UWBC deliverable data can be downloaded at the UWBC Facility Files download page. Log in using your UW NetID (for UW-Madison users) or email address and password (for external users).

SFTP download:

There are two options for SFTP downloads:

  1. Any UW-Madison user can log into our server download.biotech.wisc.edu using UW NetID credentials. This will give you access to all deliverable data that has been created for you by UWBC facilities. Only SFTP connections are allowed, SSH to this server will not work. At this time only UW-Madison users with UW NetIDs are supported for this type of SFTP transfer. Uploads to this server are not allowed.
  2. BRC account users can log in using their BRC account credentials. This will give access to the same deliverable data, plus the contents of your BRC home directory. This uses a different server, brchome.biotech.wisc.edu, which is reserved for data transfer purposes only.

For security reasons, we only allow SFTP transfers from UW-Madison networks. Remote users must use the web portal or connect to the campus network using the DoIT VPN service. Contact the DoIT help desk or your local IT support if you need help with the VPN service.

SFTP instructions for Windows:

  1. Download and install WinSCP.
  2. When you start the application you will get a dialog called WinSCP Login.
  3. Enter download.biotech.wisc.edu or brchome.biotech.wisc.edu under Host name (see the difference between the servers above).
  4. Enter your BRC account username and password.
  5. Make sure SFTP is selected under Protocol.
  6. Click Login.
  7. If you get a message saying "The server's host key was not found in the cache..." click Yes.

If you need more assistance see this page: Guide to setting up WinSCP (Windows File Transfer)

SFTP instructions for Macs:

  1. Download and install CyberDuck.
  2. Select Open Connection under the File menu.
  3. Select SFTP from the drop down menu.
  4. Enter download.biotech.wisc.edu or brchome.biotech.wisc.edu under Server (see the difference between the servers above).
  5. Enter your BRC account username and password.
  6. Click Connect.
  7. If you get a message that says "Unknown host key" click Allow.
Use the Help menu in the application if you need further assistance.

SFTP instructions for Linux:

CentOS 7 and Ubuntu 16 include newer versions of the command line SFTP client that support autocomplete and recursive downloads (the SFTP client is part of openssh). CentOS 6 has an older version that does not support these features, which makes the SFTP client very hard to use. There are also GUI clients available for Gnome, KDE, etc.

Globus Connect:

Please follow these instructions to allow you to download data from the UWBC Globus Connect server using CILogon. Globus Connect is a very fast, convenient method to transfer large amounts of data. CILogon allows members of the InCommon Federation to log in using their home institution credentials.

Install the Globus Connect application on your computer and create a Globus account. Mac, Linux and Windows versions are available.

1. Log into https://cilogon.org/. You will need to choose your home institution from a list. If you find it, log in. If it isn't listed your institution may not be a participant. If you have a Google account you can use that instead. If you have no usable accounts you can still use the UWBC Facility Files web download page.

UW-Madison users can skip to step 4

External users:
2. Once you have logged in you should see a “Certificate subject” listed. There is no sensitive information here, it is just an identifier. The line should start with "/DC=org" and end with a code with a letter and some numbers.

It will look similar to this. Copy the entire line and email it to us:

Certificate Subject:   /DC=org/DC=cilogon/C=US/O=University of Wisconsin-Madison/CN=George Washington A53556

The page may include a button to Get a New Certificate. There is no need to do that, just send us the Certificate Subject.

3. You will be notified by UWBC staff that your account is ready you can log into Globus Connect to download your files.

4. You will need to Install the Globus Connect application on your computer and create a Globus account. Mac, Linux and Windows versions are available.

6. To log in, open Globus Connect application. Choose use your existing organizational login and select your home institution. To find the UWBC endpoint that contains your files, search in Globus Connect for UW-Madison Biotechnology Center - Internal Users or UW-Madison Biotechnology Center - External Users.


NOTES:

  • Please use a WIRED connection to transfer large amounts of data.
  • Make sure you have enough hard drive space to hold the data.
  • You can't use the brchome server to analyze your data, just to download it. There are no data analysis applications installed.