Ubuntu at Work in the Medical Office
"So I've installed Ubuntu on my office workstations. What do I do next?"
- Installing Printers and sharing them on the network
- Scanning work flows
- Working with PDF
- Setting up shared network folders
- Accessing shared network folders
- Essential Firefox security tweaks
- Back up Your Default Firefox Configuration and Bookmarks
- Install the Extended Support Release (ESR) Version of Firefox
- Word-processors in Ubuntu
- Managing updates
- Setting up a screen lock
- Securely deleting data
How to install the vast majority of printers in Ubuntu:
- Step 1: Plug your printer in and connect the USB cable.
- Step 2: Switch it on.
Ubuntu will generally figure out what to do behind the scenes, find out the model of the printer, assign the correct driver, and let you know that your printer is installed and ready to go.
However, in the few cases where this doesn't work, try running your system updates, and try again (if it is a brand new printer). If you have an HP printer then it will usually be recognized with no fuss. HP actually offers an additional printing configuration toolbox you can install through the Ubuntu Software Center:
In the rare cases where Ubuntu doesn't have a built-in driver for your specific printer, then you will need to find the right driver for your printer. Most printer manufacturers post their Linux drivers on the Internet. In my case I had to grab the driver for my Brother QL series label printer from here. I followed the clear posted instructions and the printer works perfectly.
Now that you have your printers working, you might want to share some of them on the network, so you can print to them from other workstations. From your menu, go to Printing > Server > Settings and you will see this Window:
Point of caution: don't share exam room printers on the network. You don't want to end up accidentally printing a prescription for a patient to the exam room next door. Also when documents fail to print, check for hung print jobs first, before trying to re-install printers (just like in Windows)...
Before we even begin...you need the right hardware. While Ubuntu will automatically detect most commonly used scanners on the market, do yourself a favour and get a Fujitsu Scansnap S1500 scanner. It isn't cheap, but it is worth every penny! It scans blazingly fast, does double sided scanning with one pass (duplex ADF scanning) and can be dismantled easily to clear jams. Most medical offices I know of are using this scanner
How to install a Fujitsu ScanSnap S1500 on a computer running Ubuntu:
- Step 1: Plug the scanner in and connect the USB cable.
- Step 2: Switch it on.
So now that that's settled let's head over to the Ubuntu Software Center and grab the best workhorse scanning program of the many free ones out there. It is called gscan2pdf.
Once you've installed this, just open the software and connect the scanner and gscan2pdf will recognize the scanner and launch the scanning dialogue:
I find that setting the scanner to scan "line art" at 300 dpi is the best compromise between resolution, file size and speed. There are some further image clean-up tools, such as de-skew and sharpen. There is even an OCR (optical character recognition) option. We don't bother with those since it just slows the work-flow down.
For double sided pages go to the "Standard" tab and select the ADF (auto document feeder) duplex option.
This means that the page will be read with the front and the rear sensor during one pass. You can also adjust the paper size setting in the "Geometry" tab. The default setting is letter size paper. You can select legal size by simply changing the page length in mm, for example change the length from 279 mm to 356 mm.
Once you have scanned you can save. The program will save as PDF by default. Then you just follow the usual file naming and upload convention you use in your office. We find that the ScanSnap scanner paired with Ubuntu Desktop and gscan2pdf makes scanning a breeze.
Users of proprietary operating systems often have to purchase programs such as Adobe Acrobat Professional to be able to edit, annotate, split, merge and otheriwise modify their PDF files. As an Ubuntu user you are spoilt for choice! There is a great assortment of free PDF reading and editing software to choose from:
Evince: This is default PDF reader software in Ubuntu, and many other Linux distributions. it is a bare bones, but super fast PDF reader, and gets rid of a lot of the bloat that slows down Adobe reader. Out of the box, this should be already enabled as the default PDF viewer application for Firefox (Firefox calls it "Document Viewer"). A few suggested tweaks: Hit F9 to show the side pane, then check "Best Fit" from the View menu, and finally hit CTRL+T to make the settings stick.
PDF Viewer: This is a great little Firefox add-on that lets you view your OSCAR PDF documents right in Firefox tabs or windows. You can optionally download them from there and still open them on your desktop if desired. You need this installed in Firefox to make the OSCAR Document Browser work in Ubuntu. You can get the PDF Viewer Firefox add-on from here.
PDF Mod: Available from the Ubuntu Software Center, this is a great and simple tool to merge and split PDFs using graphical thumbnail images of the actual pages. It complements gscan2pdf nicely and so gives you pretty much all the functionality available from proprietary software such as PaperPort.
Using PDF Mod, you can re-order the pages in the document by dragging the thumbnail images around. You can also delete single or multiple pages from the document, or add-in new pages from another PDF document.
Xournal: Also available from the Ubuntu Software Centre, this is a very user friendly tool for making annotations on PDF documents and embedding those as indelible electronic images.
With Xournal, you can scribble handwriting or signatures on the PDF using a touch screen, tablet or a mouse or stylus, or you can embed text boxes containing typed text. Useful for those who like signing off their PDF results this way.
Once installed, you can set Xournal as the default application to open PDFs with from Firefox. From the Firefox menu bar: Edit > Preferences > Applications Tab, then scroll to "PDF", select "User other" and browse to usr/bin/xournal on your hard drive. To change back to Evince, repeat the above process and browse to user/bin/evince.
PDF Editor: Another PDF free editing program available from the Ubuntu Software Centre, this tool lets you open text PDFs for editing. You can superimpose textboxes on image PDFs too (you can also do that with GIMP image editor)
This is a more advanced tool for PDF editing, that allows you to add text and metadata to text PDFs, and also create overlay text boxes, arrows and such in image PDF files.
Acrobat Reader: The old standby is still available for Linux users. Ubunuts don't like it much since it is quite big, slow and bloated, but if desired you can get the Acrobat Reader .deb install file from here. It will open with the Ubuntu Software Centre. To make this the default PDF reader application for Firefox: Firefox menu bar > Edit > Preferences > Applications Tab, then scroll to "PDF", select "User other" and browse to usr/bin/acroread on your hard drive. To change back to Evince, repeat the above process and browse to user/bin/evince.
Setting up Network Shared Folders:
Setting up folder sharing on Ubuntu is relatively easy, when compared to doing this in Windows, but it still requires a few steps.
Start by creating your new folder you'll be sharing (right click and select "Create New Folder" on the desktop or in the File Browser window), then give it a name. I have named my new Folder "New Folder", but you should give yours any name you would find useful. Now I want to share it on the network. So right-click your new folder and select "Sharing Options".
You will now see this window:
Check the "Share this folder" box above, and you will be prompted to install the sharing software (which is called "Samba" - because it makes Ubuntu samba with other machines, even Windows machines).
Click Install service.
Click to "Add the permissions automatically"
Presto! Behold your newly shared folder on the Desktop!
Accessing Your Shared Folders on the Network:
You can now go to any other Ubuntu machine on the network. On the remote machine, open the Ubuntu software Center and install the "Personal File Sharing" package, to be able to access network shares:
...and now you can browse to the folder you set up for sharing on your other computer. You do this by opening the File Browser (the file browser/explorer in Ubuntu is also known as "Nautilus") and click on the "Browse Network" item in the left side pane.
You then might be prompted for a password again, depending on the permissions you have set for that share:
If you are using older Ubuntu versions with the "classic" desktop, then, once you have mounted the shared folder to another computer, an icon for that shared folder will appear on the desktop of the remote machine. The new Ubuntu Precise with the Unity desktop does not do that by default, but you can enable that in settings.
As a security measure, Ubuntu does not allow persistent network shares, so you will have to browse back to the shared folder from the remote machine and remount after each reboot. Generally you don't have to reboot your office machines very often, our office computers maybe get rebooted once a month or so.
It is generally a good idea to use strong passwords, and change your domain names from default. Please note that while you can easily access shared Windows folders from an Ubuntu machine, doing it the other way around (exploring to an Ubuntu share from a Windows PC) is not so straightforward.
Essential Firefox Security Tweaks:
Firefox is a modern and secure browser with some advanced privacy and security settings. These are useful when working in the medical office since you want to keep your system secure when connected to outside websites (for example while searching for medical information). Also, when you open scanned documents from your patients files, these documents actually download from the OSCAR server into the Downloads folder on the computer you are working on. You really don't want to leave traces of patient information lying around on your workstation computers. You EMR data should live in your securely backed up OSCAR server and nowhere else. On a fresh install of Firefox you want to set the Privacy setting as follows:
Go to Edit > Preferences (Tools > Options in Windows). If you're running Ubuntu 12.04 LTS, you can just press the Alt key and type "pref" to open the Preferences dialogue. Click on the "Privacy Tab". You will see this window:
To tighten up your browser security settings you need to make a few changes as follows:
Select The "Use custom settings for history" item in the History drop-down, and be sure to check the "Clear history when Firefox closes" box. Choose to accept cookies, but to delete them when Firefox closes. The "Tell websites I do not want to be tracked" option is a feature of newer Firefox updates. If you are running the trusty version 3.6 of Firefox you will not yet have this.
Now click the "Settings..." button next to the "Clear history when Firefox closes" checkbox, and you will see this window:
Make sure you have checked the boxes to clear the download history and the cache. This way all the documents that have landed in your workstation computer's download folder will be cleared out when you close Firefox. Clearing the Firefox cache regularly is also important for glitch free OSCAR in-box operation.
For a more in-depth tutorial on Firefox tweaks click here.
In Ubuntu, it is actually very easy to back up your default Firefox settings and transfer them to other workstations. The settings, including all your bookmarks/favourites, your extension and add-ons, security certificates and your set-up preferences are all kept in a configuration folder located at ~/.mozilla. So what you do is click the manila folder icon in the unity launcher, just above the Firefox Icon, to open the Nautilus file browser (it should open to show the contents of your home folder by default). Then press CTRL+H to reveal hidden folders (same shortcut as in Windows). In Linux however, hidden folders are identified with leading period/dot in front of the file name. Your Firefox configuration files are kept in a folder called ".mozilla". Inside .mozilla you will find two folders. One called "firefox" and one called "extensions". Those are what you're looking for!
Once you have set up your Firefox the way you like it, you would then simply copy these two folders to a secure backup location, such as a secured/encrypted USB stick, a cloud backup space (your Ubuntu One account, Google Drive or Dropbox). Remember to replace them with updated versions regularly if you make changes to your default Firefox setup. If your Firefox configuration includes security certificates (to access Excelleris or remote access hospital information systems for instance) then you should be sure to keep the files in a secure location.
Then, when it comes to installing a new machine or re-formatting an old one, all you have to do to restore your complete configuration, is launch Firefox on the fresh Ubuntu install once to create a new initial configuration file, and then close it again. Then, navigate to home/.mozilla in the new install (remember CTRL+H) and replace those two folders above with your backed up versions you copied to your USB stick or cloud space. And you're done! No more setting up Firefox from scratch on each new workstation...
Stability is important when it comes to your work application platform. Firefox users however are generally faced with such a furious flurry of updates, that a certain amount of update frustration sets in, and Firefox on Ubuntu is unfortunately no exception. This is bothersome for OSCAR users since some of OSCAR's functions can get quirky in newer Firefox updates. Luckily, the folks at Mozilla seem to have heard our cries of anguish and have created a longer term support version of the browser to soothe our frayed nerves.
On Ubuntu you can actually run several different versions of Firefox on the same desktop, using the same default FF configuration file! (Just not necessarily at the same time - I'd advise to have only one version of Firefox open at any one time)
- To install Firefox ESR, here's what you do: Navigate to the Firefox ESR download page and grab the English version of the ESR release (scroll down the list for the latest ESR release, and make sure you pick the right one for your desktop operating system). Save to your Download folder. Now create a new folder inside your Home Folder Called "FirefoxESR". Navigate to your Download folder and right click the zipped .tar file, open with Archive Manager, and extract into your newly created "FirefoxESR" folder.
- To launch it: All you have to do is run ~/FirefoxESR/firefox/firefox. Meaning that you navigate to your home folder, click to open your FirefoxESR folder, then click to open the "firefox" folder inside that, and then find the binary/executable program file called "firefox" and click that. This will open Firefox ESR! Note that, because the new install of Firefox will still refer to the same configuration file at ~/.mozilla, the new Firefox ESR version will remember all of your old add-ons and bookmarks automatically.
- To create a desktop shortcut: You know that binary file called 'firefox' we talked about above, the one you just clicked to open Firefox ESR? Well, right-click it and select "make link". This will create a shortcut launcher icon in the same folder, with a little black arrow at the right bottom of it. Now drag that to the desktop. Easypeasy!
- To make your Firefox desktop icon pretty: It helps if you identify the ESR version of Firefox with an icon image that looks different from the regular Firefox icon. you could download either of the icons images below (just right click and save to your pictures folder). Then mouse over to your desktop shortcut icon you just created above, right click it, select "properties", and then click the picture placeholder to browse select the icon image you just saved from here. Right click it again and select "rename". Call it "Firefox ESR"
- To launch Firefox ESR at startup: Go to your dash (click the Ubuntu icon left top, or hit your "Super"/Windows key) and type startup. Open the "Startup Applications" utility. Click 'Add' to create a new startup program. Call it "Firefox ESR", and browse to the same binary file you clicked above to launch Firefox ESR before (at ~/FirefoxESR/firefox/firefox). Now Firefox ESR will open automatically when you log in.
- Note that you might have to update some of your add-ons, such as Greasemonkey, if you switch between different versions of Firefox.
The default office productivity suite in Ubuntu is "LibreOffice". This is the new fully open-source reincarnation of the now dated "Open Office". The word-processor component is Libre-Office Writer. This does pretty much everything MS Word can do, and a few extra things too, such as one click PDF export. What we do is save our default clinic letterhead file in odt (open document text) format in our OSCAR eDocs folder (as a "desktop" category item), open that on whatever office workstation we need it on, and do a 'save-as' with a new file-name. Then you can copy and paste info into the new document from the E-chart and format away.
There are a couple of tweaks users seem to ask about often with LibreOffice:
1) Microsoft fonts: "Hey, where's my Arial!" is a cry of dismay often heard from new Ubuntu & LibreOffice users. What most people don't realize is that those widely used fonts, such as Arial, Times and Courier actually belong to Microsoft Corporation and are copyrighted under the name TrueType (tm) fonts. You have to sign an "end user license agreement" (EULA) for the privilege of using them. While there is a bewildering multitude of free and open fonts available, some people really do miss their Microsoft fonts and look for a way to install those in LibreOffice. Luckily there is an easy solution. Go to the Ubuntu Software Center and search for "Ubuntu Restricted Extras". Click install and sign the EULA when prompted. This will get you system support for a bunch of commonly used applications and formats with restricted copyright (mp3, avi, mpeg, TrueType, Java, Flash, Codecs).
2) How to save documents in MS Word format (doc, docx): LibreOffice Writer saves documents in the free "odt" (open document text) format by default. It can open a wide variety of other formats, including old and new MS Word and Word Perfect formats. Furthermore the newer versions of the MS Word, Word Perfect and Pages programs, as well as Google Docs, can open .odt files seamlessly, but the older versions of MS Word cannot. For people how have to create word processor documents that have to be opened on computers running older MS Word versions, this can be a problem. Luckily LibreOffice Writer can be set up to save documents in MS Word format by default:
What you do is open LibreOffice Writer, then go to Tools>Options, expand the Load/Save item and change the "Aways save as" options for text documents from the default ODF format, to MS Word (doc) as indicated above.
Check out AbiWord: If you are running older hardware, then a great light-weight alternative to the mighty-yet-resource-heavy LibreOffice is another free open source word-processor called AbiWord. It is available from the Ubuntu Software Center. It is has everything you need, complete with formatting options, spell checker, and yes, it can save files in MS Word (doc) format too.
OSCARLetter: OSCAR actually has a built-in rich text letter editor that can function as a word processor, complete with built-in letterhead and form letter templating ability. This way you can generate letters right from the EMR in the patients' E-chart. To learn how to install it on your OSCAR system and how to use it, click here.
Managing Ubuntu System Updates:
A new out-of-the-box installation of Ubuntu is set up to update itself every every day by default. There are pros and cons about doing rolling updates this way. On the pro side, you know that your system always has the latest updates. From a security point of view, you know that you will always get the latest security patches, in case new vulnerabilities are identified and fixed by the Ubuntu developers. One of the reasons why there are virtually no viruses for Linux computers out there in the wild, is because the actual Linux operating system kernel updates itself every two weeks. It is impossible to write a virus for the Linux kernel, have it embed itself and then expect it to propagate itself widely, since people continually update their systems.
On the downside, rolling updates can also lead to increased system instability, and applications will suddenly crash unexpectedly. Windows users will have experience with this. If you want a rock solid system, you make sure everything works, and then you disable the automatic updates. The Ubuntu derivative distribution Linux Mint owes much of its current popularity to the fact they don't keep their users at the bleeding edge of updates, and instead put new "upstream" Ubuntu updates through a further vetting and testing process before pushing them to the user base, resulting in better stability.
While this is a personal decision, the best solution in my mind is to have a compromise between regular updates and stability. So I would suggest disabling automatic updates on your workstations, as long as you go around to all your workstation computers once a month or so and run updates manually, after you've tested them on one workstation, or in a VirtualBox install of Ubuntu.
How to disable automatic updates on Ubuntu: Open your Update Manager (On 12.04 press your Super/Windows key and type "update", in older Ubuntus with Gnome, look for it in your menus). You will see something like this:
Click the "Settings" button left bottom of the window:
Set the drop-down menu to "Never" notify of new updates automatically.
Please note that you have not disabled updates altogether. You've just disabled update prompts. You can still go in manually and run updates whenever you want.
Updates versus Upgrades: Ubuntu distribution upgrades are different from regular rolling updates. Regular updates are small incremental improvements, bug fixes, tweaks and security updates applied to the existing installed configuration of a specific version of Ubuntu, whereas new distribution upgrades are themselves new major versions of Ubuntu. A new distribution upgrade of Ubuntu might include completely new features and new bundled combinations of software programs (think Windows Vista versus Windows XP). The developers release a new major Ubuntu distribution upgrade every 6 months in April and October. The April release every two years is called the LTS (long term support) release. LTS upgrades are specifically tuned towards large scale deployments and they are built to be stable and fast. They are supported for 5 years. Regular upgrades on the other hand tend to contain more new cutting edge stuff that could lead to hardware and software compatibility problems on certain computers. They can also contain resource heavy features that might slow down older hardware.
We therefore recommend that you stick to the latest LTS release of Ubuntu on your office workstations and don't upgrade to new regular distributions every 6 months. For trouble free computing, you want your office network to be rock steady and about as exciting as your average toaster.
Once a new LTS upgrade has been released, then you can take your time to test it and decide if it suits your office machines. There is nothing wrong with running your office machines on a given LTS release for the duration of the 5 years of support. If you want to experiment with cutting edge Ubuntu releases, then rather do that on your home laptop, or, preferably, in a virtual machine.
How to turn off notifications for new distribution upgrades in Ubuntu:
Open your Update Manager and set the relevant drop-down menu to "Notify about long term support versions only".
Setting up a screen lock:
The screen lock is actually already set up in a default install of Ubuntu. This is described here on our "Tips and Tricks for Ubunuts" page.
Many people who use computers every day assume that when they hit the delete button, and then empty their recycle bin/ trash can, that the information is actually gone. This is not actually the case. The information is still sitting on your hard drive. It has merely been un-associated from the file table, so the file browser will ignore it. This applies to all types of operating system (Windows, Mac, Linux etc.).
There are many types of specialized software out there that will easily let you un-delete and restore information that you thought was permanently deleted. As mentioned above, you really don't want to leave traces of patient information lying around on un-encrypted network hard drives. There have been one or two scandals in the past when old computers recycled by medical offices were found to have medical patient information on their hard drives.
In order permanently delete information from your hard drives, you actually have to over-write it with random data. There are a few different utilities in Ubuntu to do this with, but the one-stop shop for all platforms (Win, Mac and Linux) is a free program called BleachBit. You can install it on your Ubuntu machines from the Ubuntu Software Center.
The BleacBit interface is very simple to use, and it lets you accurately fine tune exactly what it is you want to delete in your system. You will be prompted about whether you want to "overwrite files to hide contents". This is exactly what you want to do. BleachBit will clean applications such as Firefox, Chromium and Thunderbird too.
It is a good idea to go around to all your workstations from time to time and manually run BleachBit on them. Pay attention to the warning prompts though, when selecting specific items. For example overwriting all the free space of a new 1TB hard drive with random data can take several hours to run. So may leave that option un-selected by default, and run it only on a computer you are about to move out of the office, or retire.