Frequently Asked Questions (FAQ)

Working Remotely
Procedures for using Zoom

Related Topics

Backup processes

Workstations supported by the Biostatistics IT staff at 2525 West End Ave are backed up in different ways depending on the type of system.

Linux workstations

Linux workstations are backed up daily. Once a day, each user's /home directory is saved to a backup staging server. The files on the staging server are subsequently copied to tape. This is not a permanent archive. We can usually recover a file from up to 3 month ago, but not earlier. The backup tapes are reused and the older backups get overwritten. Linux users may contact the IT staff for assistance recovering files.

Windows workstations

Windows computers are not backed up by the department. Windows users can protect important files from loss by using network attached storage (NAS). Each department member is allocated space on servers that are operated and backed up by VUMC IT. Each user maps their share to a drive letter on their workstation. For Windows users, the normal versioning tools allow the recovery of the earlier versions of a particular file. Box.com storage may also be used. If you do not have access to an NAS share, contact the IT staff and we will get you set up. One can contact the IT staff for help recovering a file from a mapped share.

Macintosh workstations

Macintosh computers are not backed up by the department. Macintosh users can protect important files from loss by using network attached storage (NAS). Each department member is allocated space on servers that are operated and backed up by VUMC IT. Each user connects to their share from their workstation. One can contact the IT staff for help recovering a file from a connected share. Box.com storage may also be used. If you do not have access to an NAS share, contact the IT staff and we will get you set up.

Laptops

Laptops are not backed up by the department. However, users can protect important files from loss by using network attached storage (NAS). Each department member is allocated space on servers that are operated and backed up by VUMC IT. Box.com storage may also be used. If you do not have access to an NAS share, contact the IT staff and we will get you set up.

Data privacy note

Data containing private health information or other protected information should not be stored on individual workstations or laptops. VUMC policy directs us to store protected data on appropriately configured servers or on Box.com storage. Contact a member of the IT staff if you have any questions.

How to map (or mount) a network share

Let's assume we want to map (or mount) a network share that is being served by a Windows or other SMB server. Lets call the server "i10file.vumc.org" and the share "biostatistics/someshare". The full share name would be "\\i10file.vumc.org\biostatistics\someshare" or "//i10file.vumc.org/biostatistics/someshare" depending on the type of system we are connecting from.

Also assume that your VUnetID is "vunetid".

You will need to make a VPN connection first if your computer is outside VUMC or is connected to the network wirelessly and is not using the vumcemployee network.

Macintosh

To connect using a Macintosh do these steps (If you are off campus or connected using the VUMCguest wifi network you will need to make a VPN connection first):

  • Open the Finder
  • Click on the “Go” menu and select “Connect to Server…”
  • For Server Address enter (for example) “smb://i10file.vumc.org/biostatistics/sharename” and click the + button
  • Click the Connect button
  • When prompted enter “vanderbilt\vunetid” for the username and your epassword for the password (where "vunetid" is your VUnetID).
  • Select the “Remember this password” box
  • Click the Connect button

Once the share is mounted, the mount point will be “/Volumes/vunetid”.

Linux (credit: https://www.computerhope.com/issues/ch001636.htm)

Access a Windows shared folder from Linux, using Nautilus

Many Linux distributions, especially those that use the GNOME desktop environment, use the Nautilus file manager. If this is what you're using, you can follow these steps to access your Windows shared folder:

  • Open Nautilus.
  • From the File menu, select Connect to Server...
  • In the Service type: drop-down box, choose Windows share.
  • In the Server: field, enter the name of your computer.
  • Click Connect.

Alternatively, in the Nautilus address bar, you can type smb://ComputerName/ShareName and press Enter. For instance, when you created your Windows Share, if the share name was listed as:

\\i10file.vumc.org\biostatistics\ShareFolderName

Type

smb://i10file.vumc.org/biostatistics/ShareFolderName

and press Enter. Note the smb: at the beginning, and that on Linux you should use forward slashes instead of backslashes.

Once the share is mounted, the mount point will be “/run/user/username_or_userid/gvfs”. For ease of access a link can be created to the mount point.
ln -s /run/user/<username_or_userid>/gvfs ~/.gvfs

Access a Windows shared folder from Linux, using the command line

You can also access your Windows share from the Linux command line using the smbclient program.

  • Open a terminal.
  • Type smbclient at the command prompt.
  • If you receive a "Usage:" message, this means smbclient is installed, and you can skip to the next step. If the command is not found, however, you need to install smbclient. Follow these steps to install it.

If you use the apt package manager, which is the default on Linux systems such as Ubuntu or Debian, you can use the sudo apt-get install smbclient command.

  • With smbclient installed, you can connect to your Windows share using the command smbclient //ComputerName/ShareName -U Username. For instance, if your VUnetID is doejoh, and your Windows share network name is //i10file.vumc.org/biostatistics/ShareFolderName, use the command smbclient //i10file.vumc.org/biostatistics/ShareFolderName -U doejoh. Notice that the Linux command uses forward slashes instead of backslashes).

  • Enter your password.
  • Once authenticated, you are placed at an smb: \> prompt.
  • Here, you can use the ls command to list files.
  • Use the command get filename.ext to transfer a file named filename.ext from your Windows share to your Linux machine, for example.
  • Type help for a listing of further commands.
  • Type quit or exit to return to the command prompt.

Windows

  • Open the file manager
  • Right click on Computer and select "Map network drive..."
  • In the Map Network Drive window that comes up, select an available drive letter. Enter \\i10file.vumc.org\biostatistics\someshare in the "Folder" box.
  • If you are using a computer that is logged on the Vanderbilt DOmain, click Finish and you are done.
  • Otherwise, check the box beside "Connect using different credentials" and click the Finish button.
  • In the User name box enter "vanderbilt\vunetid" and enter you epassword in the Password box. Set the "Remember my credentials" check box if you like.
  • Click OK. That should be it.

Multi-Factor Authentication (MFA)

You will be able to choose how you receive the MFA passcode you'll need when logging on to resources that require multi-factor authentication. These choices are:

  • as a text message - Simplest. You will get a passcode sent to you by text. You type in the passcode to complete authentication.
  • via the MobilePASS+ application on your smart phone - The resource requiring multi-factor authentication will send a request to the smartphoneMobilePASS+ app. You click "ok" in the app, and the authentication will complete. If you use this option, pick the "purple client". The "orange client" is for clinicians who prescribe controlled substances.
  • on a hardware token (eToken) - the hardware eToken is a gadget you can carry with you (on your keychain, for example). It displays the passcode you need to complete the authentication and you type it in. I recommend this if you don't have a smartphone, don't want to add another app to your phone, or just want to carry additional gadgets. The eToken is free but will cost $30 to replace if lost. If during the MFA setup you answer that you have no smart phone or cell phone, you can choose to use a physical security token. VUMC will ship you a physical token (or you can pick it up). The option to choose a physical token is not given to you unless you answer that you have no phone.

Virtual Private Network (VPN)

Go to http://www.vumc.org/enterprisecybersecurity/vpn. The instructions are quite complete and detailed, but need to be read carefully if the process is to go smoothly.

Where can I find Skype for Business and telephone information?

https://it.vanderbilt.edu/services/catalog/collaboration_and_communication/collaboration/Skype_for_Business.php

If I have 2 email accounts, how do I redirect email to the correct account?

If you want your @vanderbilt.edu address to be the primary:

  • Using https://email.vanderbilt.edu , log on to your @vanderbilt.edu email account and remove any email forwarding or redirecting rules that may exist.
  • Next, using https://outlook.office.com, log on to your @vumc.org email account and set it up to redirect incoming email to your @vanderbilt.edu address.

If you want your @vumc.org address to be your primary address then reverse the process:

  • Using https://outlook.office.com, log on to your @vumc.org email account and remove any email forwarding or redirecting rules that may exist.
  • Next, using https://email.vanderbilt.edu, log on to your @vanderbilt.edu email account and set it up to redirect incoming email to your @vumc.org address.

By “primary” address, we mean the address that you consider to be your main address. It is the email account that you send email from and check for incoming email.

Or, one could skip all this forwarding business and just remember to check both email accounts.

Another option is to not do any forwarding, but instead, put an autoresponder on the email account that you do not want to use. The autoresponder would reply to any email coming in to that account and inform the sender that you don’t want to receive email at that address. It would also mention your preferred address.

Also, see these notes on how to redirect email from your @vanderbilt.edu address to your @vumc.org mail box.

How to get a MacBook to join VUMCEmployee wireless network?

The process documented on the VUMC IT web site does not seem to work. Here's what I have done that does work.

A zip file downloads. Navigate to the downloaded folder, expand the zip file, and run the installer.

Working with "big data" in R

Here are links to some resources

How does a new employee get information about getting started in Biostatistics?

Our wiki has a "Getting Started at Vanderbilt Biostatistics" topic. This topic is a collection of what one needs to know to get started at Biostatistics. The focus mainly on Information Technology and related subjects. Vanderbilt Information Technology has a Getting Started: Get up and running at Vanderbilt page that has some helpful information.

Where can I get information about cyber security?

See the Data Security section of Getting Started at Vanderbilt Biostatistics topic.

How do I share data with a statistician

Review email marked as spam

Where can I find information about Vanderbilt's high performance compute cluster (ACCRE)?

Where can I get information about the department's computer server resources?

How do I use a VPN client to connect to the VUMC network from off campus?

See https://www.vumc.org/it/vpn for instructions to download, install, and configure the VPN client.

Where can I find information about logos and templates?

See Biostatistics Logos and Document Templates

How do I get a Shiny app hosted?

How do I deploy a Shiny app?

We have set up a Shiny server on our statcomp2 server. See for example https://statcomp2.app.vumc.org/VisualPruner/

To install your shiny app on the statcomp2 server, do the following:

  1. Develop your shiny app and get it working on your workstation.
  2. Ask the Biostatistics IT team for an account on statcomp2.emp.vumc.io if you don’t already have one.
  3. Log on to your statcomp2 account and make a new sub-directory called /home/vunetid/ShinyApps/ (where “vunetid” is your VUnetID)
  4. Make an appropriately named directory in /home/vunetid/ShinyApps/. For example, if your app is called "MyApp1" then make a directory /home/vunetid/ShinyApps/MyApp1.
  5. Copy your Shiny application to this new directory.
  6. Let us know when you are done at biostat-it@vumc.org. A link has to be added. After that your application will be live. Also, let me know what packages your app uses. We might need add them.

Once configured, your app's URL will be https://statcomp2.app.vumc.org/MyApp1.

Browse files on a server or network share

Automount windows share in Ubuntu

See http://stackoverflow.com/questions/33566227/automount-windows-share-in-ubuntu-14-04-lts

Lets say there is a share being served from a Windows computer that we need to use regularly. We'd like to mount that share on our Linux computer.

In the notes below
  • $SERVER is the name of the server
  • $SHARE is the the name of the share to be mounted
  • $VUNETID is the user's VUnet ID
  • $EPASSWORD is the user's ePassword
  • $MOUNTPOINT is a directory serving as the local mount point. This is typically named the same as the share but can be any directory that the user can write to. This directory must be empty.

Create a mount point. This is just a directory the share is mounted and where it can be accessed on the Linux computer.
mkdir /home/$VUNETID/$MOUNTPOINT

Add this line at the end of the /etc/fstab file
//$SERVER/$SHARE /home/$VUNETID/$MOUNTPOINT cifs credentials=/home/$VUNETID/.smbcredentials,uid=$VUNETID,domain=vanderbilt,iocharset=utf8,_netdev,sec=ntlm 0 0

Create a file called /home/$VUNETID/.smbcredentials. Put these lines in that file.
username=$VUNETID 
password=$EPASSWORD
domain=vanderbilt

Protect .smbcredentials (it contains a password!).
chmod 600 /home/$VUNETID/.smbcredentials

Mount the share
sudo mount -a

How to operate the Garden Room audiovisual system

How do I operate the projectors in the 2525 conference room and classroom?

To turn the system on, press the VGA or HDMI button as appropriate.
  • Use the HDMI button for the conference room Linux computer, Apple TV device, or anything else connected to the podium switch box. This could be a speaker provided laptop.
  • Use the VGA button for anything connected to the black extension cable (most likely a speaker provided laptop).

It will take a minute or two for the system to lower the screen, turn on the projector, and warm up. Please press the button only once.

To turn the system off, press the DISPLAY OFF button. It will take a minute or so for the system to raise the screen and shut down. The DISPLAY ON and DISPLAY OFF lights will flash during the shutdown process. Please press the button only once. Please turn the system off when you are finished. Contact Dale or one of the IT Team if you have problems.

There is no need to press any of the other buttons.

projector control panel

What are the network addresses (hostnames) for the department's printers?

If you want to install your own printer drivers you will need to know the network address of the printer you wish to install. Most installation tools will attempt to find all the printers on the network and let you pick one. This rarely works because there are so many printers around and sometimes the printer you want is not found. It is better to specify explicitly the printer in question. All installation processes I have seen provide an option to specify the printer web address directly.

The type of printer can be also be found there. You'll need to know that when installing the printer. You'll also need to know the printer type if you have to download a driver from the manufacturer.

The procedure for installing these printers on the Linux computers is on the workstation setup wiki page.

How to install printers...

You will need the printer host names:  http://biostat.mc.vanderbilt.edu/wiki/Main/PrinterHostnames

...on the Linux workstations

See the workstation printer set up instructions

...on Windows 7 computers

See Windows instructions for installing printers (pdf)

...on Macintosh computers

See Macintosh instructions for installing printers (pdf)

What are the names of the department's various Exchange calendars?

The department has a number of calendars that are used to schedule events and reserve rooms.

Events:
Calendar Name commonly used name Exchange alias
Biostatistics Department Calendar department event calendar vmcbiosta2  

Rooms:
Calendar Name location commonly used name Exchange alias
Biostatistics Conference Room 11105 WEA 2525 West End room 11105 big conference room mscbiosta1
Biostatistics Class Room 11139 WEA 2525 West End room 11139 class room mscbiosta2
Biostatistics Garden Room 2525 West End room ??? Garden Room mscbiosta5

Using the Pidgin Instant Messaging Client with Lync

Using the Pidgin Instant Messaging Client with Lync

Letterhead templates and images

See Audrey Carvajal if you need letterhead templates in Word, PDF, or other formats.

How do I "de-identify" a data set to remove private information?

What are the LDAP directory settings to use with Thunderbird email client?

  • Edit menu ... Accounting Settings
  • Select the Composition & Addressing item
  • Click on the Edit Directories... button
  • Define the directory server like this:
    • Name: VUdirectory
    • Hostname: vudirectory.vanderbilt.edu
    • Base DN: dc=vanderbilt, dc=edu
    • Port number: 389
    • Bind DN: blank

Use secure connection (SSL) can be checked or unchecked (I like checked)

Where are "How To" Pages on the Biostatistics Wiki?

How To Pages

What are some Stata learning resources that you recommend?

Each of these will have some information that is specific to the originating institution.

From Princeton
http://www.princeton.edu/~otorres/Stata/
http://dss.princeton.edu/training/StataTutorial.pdf

UCLA Academic Technology Services
http://www.ats.ucla.edu/stat/stata/
http://www.ats.ucla.edu/stat/stata/sk/default.htm

Economic and Social Data Service, UK
http://www.esds.ac.uk/government/docs/documents/StartingStata9.pdf

Institute of Economic Education, WWU Münster
http://www.wiwi.uni-muenster.de/ioeb/Downloads/Forschen/Pfaff/Introduction_to_Stata_with_50+_Basic_Commands.pdf

Where can I get some help with R?

See Frank's R and S-Plus Packages, Functions, and Documentation. Of interest to new R users is Terri Scott's "An Introduction to the Fundamentals & Functionality of the R Programming Language" and other lecture notes that can be found on her page. Also of interest to R users coming from SAS or SPSS is R for SAS & SPSS Users by Robert Muenchen.

Where can I find "how to" help?

There are a lot of useful how to pages on our site. See How To Pages on the Biostatistics Wiki

Where can I get some programming tips?

"I am a statistician, not a programmer." How often have you heard this? See Programming Tips For Statisticians for programming hint and tips.

Introduction to Linux

The ACCRE web site (http://www.accre.vanderbilt.edu/) has a nice introduction to Linux formatted as a PDF file. See it at http://www.accre.vanderbilt.edu/docs/IntroductionToUnix.pdf. There are a few details that are specific to ACCRE, but for the most part it is appropriate for our environment as well.

How do I enable the Jump Auto Completion feature of the Biostatistics web site?

By default, the Jump Auto Completion feature is not enabled if you are not connected to the Vanderbilt network. The instructions on the Topic Jump Auto Completion page.

How do I run my R program as a batch job?

The problem: If one runs a program as an interactive job (i.e. connected with a terminal session) then the job will be terminated if the interactive session gets disconnected. The interactive session will most certainly get disconnected if it sits idle without any keyboard input or video output for a while. This is a feature of the Vanderbilt network that we cannot change.

The best way to execute long running jobs is to run them as batch jobs. When running as a batch job, the process is not dependent on the existence of a terminal session. One can launch the job and log out and it will continue to run.

Let's say we have a R program called "helloworld.R".

You can execute an R script from the command line by using a command like this:

$ Rscript helloworld.r
or
$ Rscript helloworld.r > helloworld.Rout

This will execute the R commands that are stored in the file helloworld.R and write the output to a file helloworld.Rout.

But if it is a long running job then your terminal session might get disconnected before the program is complete.

One of the following techniques will allow you to run the job without the job being dependent on a terminal session.

Then use one of these techniques:

  • Use the "nohup" command to run the script, e.g.:
$ nohup Rscript helloworld.R > helloworld.Rout &

  • use the "at" command to submit the script to a batch queue, e.g.:
$ at now
at> Rscript helloworld.R > helloworld.Rout
at> ctrl-d
$

at now means to run the batch job immediately ("now"), but you can specify any time in the future. Be sure to read the man pages for nohup (man nohup) and at (man at) for further details.

How do I add fonts to a Wine installation?

One important thing to do is to install the msttcorefonts package

$ sudo apt-get install msttcorefonts

This package will give you the Arial, Comic Sans, Courier New, Georgia, Impact, Times New Roman, Trebuchet, Verdana, and Webdings TrueType fonts.

Other TrueType fonts and be installed by copying the appropriate .ttf file into the Wine installation fonts directory. For example:

$ copy /my_downloaded_fonts/symbol.ttf /home/vunetid/.wine/drive_c/fonts

How do I make the wiki edit box bigger?

The edit box used to create and edit wiki pages is pretty small and the font is too little. How can I make these bigger?

To make the edit box bigger, add two lines like these to your personal page:
   * Set EDITBOXWIDTH = 70
   * Set EDITBOXHEIGHT = 25
The 70 and 25 can be changed to suit your tastes, but these values seem to work pretty well.

In the Firefox web browser, the font size in the twiki edit box can be changed by going to the Edit menu, clicking on Preferences, then clicking on the Content item. Click on the Advanced button in the Font & Colors section. In the Fonts dialog that appears change the Monospace font size to something a little larger than the default (16 is a pretty good size).

Wiki topic naming advice

Over time several Wiki users have created topics for specific reasons but have assigned generic names to these topics (e.g. JournalClubICUD, MyLearning). There is nothing wrong with this but in some circumstances it can prevent a later user from creating a topic that needs to be fully generic. This is more important now that you can link to a topic with a short name you can publish, such as biostat.mc.vanderbilt.edu/MyTopic . It would be best if we reserved generic names for topics that are for general use that spans multiple groups. You might consider using names such as ProjxJournalClub for Project X's Journal Club.

Thanks for your consideration.

Backups

Backup are being performed for the following locations each night:

  • /home/vunetid on your personal linux workstation
  • /home/vunetid on biostat.mc.vanderbilt.edu
  • other appropriate directories on data.vanderbilt.edu and statcomp2.emp.vumc.io.

Excluding Files from Backups

If you have a external mount point in your home directory you should not have this backed up. To exclude a dir or file from being backed up place a rsync exclude rule in the file .backup-exclude
  • Example: excluding ~/mnt. Run the following command
    echo "- /mnt/" >> ~/.backup-exclude
    

Restoring Deleted Files

If you have deleted a file or collection of files and would like to restore them, please email biostat-it@list.vanderbilt.edu with the following information:

The names, locations, and dates of the files that you would like to be restored. The location will include the hostname and the directory where the file resided.

As an example, If I accidentally deleted /home/vunetid/Desktop/FinalProposal.tex from my linux workstation biostat028 on October 27, 2004, I can ask to retrieve that file as it looked on October 26, 2004 or earlier. My email to biostat-it will look like this:

    To: biostat-it@list.vanderbilt.edu
    Date: October 27, 2004
    Subject: RESTORE request

    Please restore the following file as of October 26, 2004:

    biostat028:/home/vunetid/Desktop/FinalProposal.tex

    and place it in the folder:

    biostat028: /home/vunetid/Desktop/RESTORE

    Thanks

The turn-around time on restoring files will be anywhere from 2 to 5 days. Also, If you have any questions about backups don't hesitate to email us at biostat-it@list.vanderbilt.edu.

Remote Access

  • Tools that can be used on a Windows system to access your office Linux workstation or one of the Biostatistics servers:

  • Tools that can be used on a Linux system to access your Linux workstation or one of the servers:
    • ssh
    • scp

Connecting to Linux desktop from a remote location (FreeNX)

Notes from Jeremy's "Working Remotely" seminar

LaTex Links and Notes

  • LaTex cheat sheet
  • Commands to invoke LaTex and view or print the output:
        Linux
        $ latex test.tex   # invokes LaTex, processes test.tex, and writes test.dvi
        $ kdvi test.dvi    # opens test.dvi for viewing and printing
    
        Windows (MiKTex)
        > latex test.tex
        > yap test.tex
        

Migrating from Windows to Linux

IBM has published a "Redbook" aimed at assisting those interested in migrating desktop PCs to Linux. Linux Client Migration Cookbook: A Practical Planning and Implementation Guide for Migrating to Desktop Linux provides in-depth detail on the technical and organizational challenges and includes methods for planning and implementation, according to the book's cover. The 260-page book is available for free download as a PDF file.

Why does Linux use such funny naming schemes?

This article may not give you any great answers, but it does provide a list of Linux substitutes to Windows applications.

Konqueror and pdf files

When I click on a link that points to a pdf file, I want Konqueror to use acroread to display the document. We assume that acroread is correctly installed.
  • click on the Settings menu and then the "Configure Konqueror..." item
  • Make sure the General tab has focus
  • click on the File Associations item in the left menu
  • expand the "application" group in the Known Types box and click on the the pdf type
  • in the "Application Preference Order" section, click on Add and enter the full path to the acroread application
  • click apply
  • click on the Embedding tab
  • for the "Left Click Action", select the "Use settings for 'application' group" item
  • click OK and you are done.

How should I organize my directories?

BASH questions

How do I prevent BASH from showing duplicate commands in my command history?

  • add the line to .bashrc: export HISTCONTROL=ignoreboth
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