Computing Clinic

The Computing Clinic is currently on an extended hiatus (as of 12/2013) while the department's administration structure is being reorganized. We will update this page when there is something new to report. You may be interested in the The Statistical Computing Series as an alternative.

A Discussion Forum for Anything Related to Computing and Linux.

1st Tuesday of each month at 9am in the Biostatistics Conference Room: D-2221 MCN.

We Need New Topics!

If you would like to suggest topics for discussion in upcoming clinics, just add them below, or email us at biostat-it@list.vanderbilt.edu. If you email, put "computing clinic question" in your email subject.

We used to have a topic called "The Linux Workstation Experience" that has become obsolete. We copied some of its contents into this topic for future reference. The Linux Workstation Experience topic has been deleted.

We have a Frequently Asked Questions (FAQ) page that contains a lot of questions that have already been answered. Check it out, too.

Add new stuff at the beginning.

March 5, 2013

  • Seth - Can't load Frank's distribution change in ePAC using Internet Explorer (9.0.8112.16421) . Keep getting an error "Internet Explorer has stopped working." Other (shorter) distribution changes load in IE. Using IE because it typically works better for VU created applications. FH's distribution loads using Firefox (19.0).

January 8, 2013

December 4, 2012

  • Stephania - can't print more than one page of email (OWA & Firefor) - checked 1/2/2013: it works to open email in a seperate window (double click on message) and then print. Tested with Firefox version 17.0.1 and the color1 printer.
  • WJ computer is hanging. computer replaced
  • Donna not happy with search features of Windows 7 showed her some other ways to do searches.
  • Eve having trouble printing multiple copies from PowerPoint.

July 3, 2012

  • Sherry can't print from Linux
  • Stephania printing from thunderbird
  • webcalendar
    • event creator; participant vs creator
    • bug - print friendly option
  • Audrey's keyboard is broken, maybe sticky/slow keys
  • Thunderbird - messages appear/re-appear for Donna (inbox only?)

May 1, 2012

  • DBConnect: Purchasing requests
    • Wanting one for membership and software request pages. Cole, will you please modify dbconnect to add this functionality?
    • Have eProcurement preferred vendors on purchasing requests Is it possible, Cole, to add xx and xx.
    • Have software and computer requests that employees put in go to Dale, Dale attaches specs, WJ for approval, to John for actual purchase

February 7, 2012

  • KDE client open/load delay and loss of drop down tab/menu.-db
  • Thunderbird "application is out of memory"; also, 3.1 "it's time for a change".-db
  • Office 2010 Presentation

December 6, 2011

  • Excel spreadsheet, last opened in OO, then saved in current format (xlsx) from LDS' computer; unable to open in Excel from db's computer, "converter failed to open file".-db
  • T'bird behind KRDC-db

October 4, 2011

  • E-mail groups (names listed after removal from list)--lds
  • T'bird behind KRDC-db
  • Docs opening as blanks (not from e-mail)-db

Problem & Resolution Tracking

Problem Microsoft Office Documents

  • Remove block for BO downloads (Windows)-db
  • Message, "Application is out of memory", each time upon opening Thunderbird.-db

June 7, 2011

  • Overview wiki webs (PhD2 search, MS search, main, etc.) (explained)
  • Umbrellaed protected pages (explained)
  • File organization (how deep the files?-db)
  • R:drive to T-bird-db (fixed)
  • T-bird under rdp: (KRD) on application bar-db (fixed)
  • copy/paste from Wiki to OO does not work; same to Word does work-db (OO bug)
  • Calendar authorship (no fix with current calendar software)
  • Using a wiki template (explained)

September 7, 2010

March 2, 2010

  • Email encryption?
  • Calendar delegate display issue
  • CTSA fed site printing

February 2, 2010

  • Calendar management, e.g., recurring meetings
  • Javascript removed from Admin systems (gotta put addresses in Trusted sites)
  • HTML removed from Thunderbird
  • Automated ordering ModernNash
  • Thunderbird...opening attachments (remote desktop) [i.e., sample sent to Dale/Cole 1.21.10]

January 5, 2010

  • Dolphin file management

December 1, 2009

  • should we request moving dept email from old exchange server to new server
    • old server is slow, several users had issues with password (see 11/3/09)

November 3, 2009

  • email is still slow; still ask for password from time to time, but not as often; "difficulty copying to folder, do you want to try again?"

October 6, 2009

  • from July 7, print size is still extremely small on some documents, but not on others. Why? How do we fix so I can read? (Diane)
  • any luck on back side programming when titles change or moot subject and all responsible for themselves when promoted, etc.? (Diane) It is the individual's responsibility to keep up with that.
  • Email client:
    • have to supply password repeatedly not as often
    • edits to message are saved permanently?
    • slow response still slow
  • Connected to Windows via krdc - behaves as if control key is pressed or stuck. still no fix for this

September 1, 2009

  • Caps lock (in WIndows) problem (Eve).
  • Email reminder from dbconnect for vacation / sick leave. OK
  • Webcalendar presentation (5 minutes) for October 12? department meeting
    • overview
    • print view URL for viewing on handheld
    • can we fix sync in current version? Sync from Google is problematic with many appointments.
  • (Donna, Eve, WJ) forwarded email problem. Make forwarded message body inline, not attachment.
  • Thunderbird add-ins to talk about: "thunderbrowse", folder navigation tool (name?)
  • Help users be more efficient
    • symbolic links rather than copy
    • folder organization and data management
    • email attachments and the original source file

August 4, 2009 - Discussion Topics

  • OpenOffice lacks many convenient templates like those that come with Microsoft Office (paraphrased from dk).
    • OpenOffice has a different philosophy than Microsoft Office. Microsoft includes all kinds of stuff; OpenOffice lets you choose what you want. You can get templates for OpenOffice at http://templates.services.openoffice.org/

July 7, 2009 - Discussion Topics

  • any way to set back end programing that expedites process (changing multiple Foswiki sites when an employee is promoted, name changes, departs, etc.) (dk) We don't know of an automatic way to achieve this. It was decided that it is the employee's responsibility to make sure that all wiki references to themselves are correct.
  • Where is the table of IT requests that the Admin Team added to last year (prior to the current Windows system)? Would like to have a table such as that with a resolution column to track requests. (dk) Dale will refactor this page and the Workstation Experience page. (09 Jul 2009) The refactoring has been done.
  • ePAC printout: eml attachment (see CA Biostat DA sample) Deferred until a specific example is brought
  • when printing Foswiki documents any way to avoid characters from merging together? (dk) This appears to be a bug in Firefox. I have seen numerous complaints about problems like this, but no fixes or workarounds. I am going to defer this for now since I have spent a large amount of time on this problem.
  • cleaning Foswiki - how do we know when it's ok to archive (or how to archive) a section that has not been used in a while? (http://biostat.mc.vanderbilt.edu/Presentations, http://biostat.mc.vanderbilt.edu/GrantsInfo) (dk) You pretty much have to use your judgment on this issue. The best course of action might be to check with the author and contributors for the topic in question and see what they think.

April 10, 2009 Discussion Topics

  • What do these funny words and acronyms mean? Debian, Ubuntu, KDE, Gnome, Kate, LaTex?
  • How do I install new software and updates on my workstation?
  • Converting popular file formats and Terminal commands.
  • Linux basics: file system structure, users, permissions, etc.

February 3, 2009

  • dbc intro/orientation for new employees
  • Biosketches

January 6, 2009

  • Donna - Issue in Microsoft that is not specific to Excel, though that is where first experienced. There is an assumption by the CPU that the control key is being held in a particular cell and that every move from that point is choosing or linking cells. This can last for quite a while and then will clear on its own. The same behavior has been encountered in ePAC as well. [hit the control key once seems to clear the condition]
  • Donna - Issue in Excel. Linked worksheets and summed columns and/or rows are not updating when workbooks are reopened though formulas are intact.
  • Donna, Linda and Sherry - Create remote desktop access from laptops. We will bring our laptops to the meeting!

September 30, 2008

September 23, 2008

  • WJ - Windows (admin server) freezes when printing. Computer resumes when printing is finished.
    • Can't reproduce. Most likely a network issue that has resolved itself.
  • WJ - Can't print to tray 1 (color4), printing always goes to tray 2 regardless of settings
  • Donna - Sent folder confusion in Thunderbird
    • With my current setup, sending from Thunderbird causes the sent document to be put in the "Sent" folder. If I send from the Outlook client the sent message ends up in the "Sent Items" folder.
    • fix: In Thunderbird - Edit...Account Settings...Copies & Folders...When sending messages, automatically...Place a copy in...Other. The select the correct "Sent items" folder from the drop down list.
  • Diane - Having trouble setting default tray when printing to color2 from Word.
    • A default setting needed to be changed. Change made in File...Page Setup...Paper tab.
  • Diane - Can't convince printer that she needs legal paper when printing from Excel.
    • There are a lot of settings for printing, both at the printer driver level and at the application level. With Microsoft products, it is best to leave the driver level settings as default and automatic as possible and let the application do the adjustments.
  • Sharon - R "out of memory" when running statistics on relative small data sets.
  • Sharon - sometimes can't "unlock" workstation. The fix we are using has to be redone after updating software.
  • Sharon - a highlight done in OpenOffice writer cannot be undone in Microsoft Word
    • Confirmed with OpenOffice.org 2.4.1 and Word 2003. Workaround in Word is Format menu...Styles and Formatting...Pick formatting to apply...Clear Formatting.
  • Sharon - can't see Microsoft Word comments in OpenOffice
    • Comments are called "Notes" in OpenOffice. There is a little yellow rectangle at the location of each note. One can hover over the yellow rectangle to see the note or double click on the rectangle to edit the note.

August 5 Discussion Topics

  • Discuss dbconnect updates: Who does what? What items does each team member update?
  • Discuss adding V-Net code to dbconnect
  • How does one create a meeting template in TWiki?

May 15 Discussion Topics

  • How does one save e-mail as a document?
    • right-click in the message and select "save-as"
    • or File...save as...

May 8 Discussion Topics

  • Your questions answered!

May 1 Discussion Topics

  • Understanding your computer's limits: How much memory can my application use? Estimating times for reading/writing/transferring large files, etc.
  • object.size, .Machine, .Platform, free, top, system.time, write.table, gc(), size of integers and floats.

April 24 Discussion Topics

  • I have some grant money ($1500) to buy a laptop. What's the best I can get for my money? Do you recommend a Mac or Windows/Linux dual boot? Any more info?
  • How can I print from Win4Lin on the color3 printer?

April 17 Discussion Topics

  • How do I update my Linux computer? Should I update my computer? How often should I update?
    • There's a little icon in the lower left corner of your desktop. You will only notice it when you need to update your computer, and the icon will look like a "Yield" sign. That's when you need to update, and follow the instructions on how to use Adept Updater.
    • To find new packages to install, use Adept Manager.
  • How do I know where to place a page or new topic in TWiki? (This is my question and I'll review FAQs. -Linda)
  • Explain function of brackets; are [[]] used for hyperlinks only or are there other purposes? Please provides details about ATTACH URL and function.
    • Use of brackets can be found on this page: TextFormattingRules
    • ATTACHURL is explained here: ...
  • I checked out FAQs and attempted to download RealPlayer in order to access the State of the Medical Center webcast; no luck, I'll try again!
  • In the TWiki printable view, I am unable to access the option to print duplex.
    • Probably the best way to do this is using "Print to file" on Firefox. Once you click the "Print" button, check the box next to "Print to file", and Firefox will save the page in Postscript format. Once you have the file, open it up with Kghostview, and from there, you'll have the option to print in Duplex mode.
    • Another method (for Firefox running under Linux):
      • Navigate to the page you want to print and click File...Print
      • For the printer name select "PostScript/default" and click the Properties button
      • In the Print Command box enter "kprinter" and click the OK button
      • Click the Print button
      • After a bit the KPrinter dialog box will come up
      • Select the printer you actually want to use. Many options are now available, such as duplex printing.
      • Click the print button to print the content.
  • How do I use the beamer class in LaTeX?
    • Use "Adept Manager" to install the latex-beamer package. It has loads of documentation, and loads of example presentations. From within Adept Manager", check out the "Installed Files" tab from the "Details" button. All of the documentation will be on your computer under /usr/share/doc/latex-beamer.

What is Linux

Linux is a Unix-like computer operating system. Linux is one of the most prominent examples of free software and open source development: typically all underlying source code can be freely modified, used, and redistributed by anyone. It also happens to be the default choice for Biostatistics workstations.

Read more about Linux at Linux.org, Linux.com, and popular references at Wikipedia, and the history of Linux.

The Linux Workstation Experience

Most of the computers in the department have Kubuntu Linux installed as their primary operating system. We have found this configuration to be very functional as a general office computing environment. From time to time, however, there are questions and problems that need to be addressed to make the working experience more positive.

Use this page to ask questions, complain about problems, and make suggestions. The IT staff will use this page to see what people need and act on those needs. Anyone may add to the list below and everyone is encourage to add answers if they have them. Be sure to identify yourself if you want us to check out something on your computer.

You might also want to have a look at the Department Computing and Frequently Asked Questions page.

Please prefix your questions and comments with a "Q:" so they can be distinguished from the answers.

  • Q: BA3 and some other Vanderbilt administrative tools require Internet Explorer to work correctly. What can we do about that? (from DalePlummer)
    • A: We have not found a satisfactory solution. The best we can do is install VMware on the computers that need it so that Windows can be run to support IE.
  • Q: I want to use my Lexar JumpDrive. How does that work? (from DalePlummer)
    • A: This is still a work in process. Ask someone on the IT staff to configure this for you.
    • A2 (DalePlummer - 05 Dec 2007): This now seems to work correctly for the latest versions of Kubuntu (Feisty and Gusty). If it doesn't then there is some misconfiguration and you can ask the IT team for a fix.
  • Q: I want to listen to Real Audio streams on my computer.
    • A: We have found that the Real Audio player works well for a number of audio formats.
  • Q: clicking on links to pdf files doesn't work like on Windows. What's wrong?
    • A: We have instructions for setting up Acrobat Reader on the Department Computing and FAQ page. This works really well for reading pdf files.
  • Q: I used gnumeric to make a pdf file from a spreadsheet. Many recipients of the pdf couldn't read the file; they got various errors from their pdf reader software.
    • A: What we are seeing is that gnumeric is bad at making pdf files from its spreadsheets. OpenOffice does a much better job. OpenOffice's pdf files are much smaller than gnumeric's and we had no problem reading the OpenOffice generated pdfs on either Linux or Windows computers. The answer, in general, is to use OpenOffice when you are making documents that you might want to distribute to other platforms.
  • Q: What are potential solutions for working in Linux with BudgetPro which requires Access 2003?
  • Q: How can one address slowness/cumbersomeness of VMWare when it is an emulator and cannot possibly be as versatile as the actual application?
    • A1: only use VMware when it is absolutely necessary. Most things can be done in the Linux world. (DalePlummer)
    • A2: add memory to the workstation and the allocate more memory to VMware. This helps a little bit.(DalePlummer)
    • A3: set up a Windows terminal server. Linux users can connect with krdc and get a full featured Windows session. Might be easier to maintain than VMware.(DalePlummer)
  • Q: Forms required for the Office of International Services, Human Resources, the NIH are in pdf fillable format and can only be stored in VMWare/Windows formats. What can be done?
    • A1: The Adobe Acrobat Reader program that is available for Linux works pretty much the same as the Windows version. One can read and print PDFs and fill in and print PDF forms. You cannot save filled in PDF forms with either the Windows or Linux version of Adobe Reader. (DalePlummer)
    • A2: If you want to save PDF forms with the user added data, you must use Acrobat Standard or Acrobat Professional. These are available on Windows only. (DalePlummer)
  • Q: Is there a more straightforward way than GIMP to do a screen shot?
    • A: Yes! Press the Prt Scr key. ColeBeck doesn't recommend this though, because GIMP can easily crop and re-size images.
  • Q: Electronic Personnel Action Change (ePAC) is a web application; however, one cannot simply attach an e-mail like a Windows user. The attempt to add it as a text file has been unsuccessful without having to key in the date/recipients.
  • Q: What are potential solutions for correcting formatting issues with HR forms (http://hr.vanderbilt.edu/forms/index.htm), e.g. position description questionnaire?
  • Q: When pasting content from TWiki to a document, in OpenOffice the coloration and formatting change. When using VM from work it also alters, though not as drastically. When cutting/pasting from home it is letter perfect (Office 2003). What is the solution so what you see is what you get?
  • Q: When attempting to complete the New Hire Orientation form The Learning Center requires for new hires, OpenOffice converts to two pages, changes the formatting, etc. This is a one page document in Word and all of VUMC submits a one page formatted document. How do we ensure our dept is professional and submits in standard format without lots of work arounds and time spent re-formatting?
  • Q: Neither AbiWord nor OpenOffice Writer will display references in a document that has been prepared with Microsoft Word and EndNote. I would not expect to be able to manipulate the references, but it is a little surprising that they are just not visible. Is there a work-around? (DalePlummer)
  • Q: Thunderbird normally wraps text, but sometimes incoming mail does not use word-wrap. Reply's fail too.
    • A: Add line to prefs.js: user_pref("mail.compose.wrap_to_window_width", true); (DennisMalandro)
  • Q: When working in Twiki, I have prepared candidate itineraries from home and pasted them directly into word documents. When doing this it pastes perfectly and there is no re-formatting. When attempting to do this from the office, it does not work. If in Linux, the coloration does not even paste. When attempting do this this w/VM Ware I have to log in to Twiki from Internet Explorer and though closer, it does not do exact as it does from home. Any suggestion how to eliminate extra steps and get what I see onscreen onto the word doc from the office? Sample: van der Laan (DianeKolb)
    • A: You could print/save the webpage as a PDF or just send the candidate the URL. (WillGray)
  • Q: How can we get complete ePAC printouts (seems to be printing problem).
  • Q: Grants.gov page not readable (see attachment)
Topic revision: r79 - 09 Apr 2014, DalePlummer
 

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