I am an ecology post-doc and considering switching from Windows to Linux for my main work computer (I am not a mathematical modeller). I have used Linux before and I am aware that, with effort, one can accomplish most any task in Linux that one can in Windows but I have not tried to convert my whole work computer over. And sometimes making a specific type tool/application work or share files with colleagues' tools (likely Windows based) can take a lot of effort/time or be error prone. As academics we all have limited time to troubleshoot issues that might appear optional.

So, my question here is for people who have made this switch or seriously considered it: what are the specific main challenges you encountered (which types of applications/tools or other issues) in making this switch?

I'm especially interested in word processing, spreadsheets, databases, statistical software, plotting and presentation software, reference management, communication, and any other applications that allow you to fulfill key responsibilities as biology faculty. I know there are various ways to port/emulate/etc Windows applications into Linux (e.g., Wine), but I'm interested in approaches that don't simply use that for every application I'm used to in Windows. And I'm asking about what challenges you had transitioning (or why you choose not to) rather than just asking for a list of Linux applications that fulfill these needs (that said, do mention specific applications if you think they are less well known).

(I'm trying to keep this narrow and not about the benefits of either OS over the other - no need for a Linux/Windows flame war. I've also tried to prevent this from being an opinion oriented question by asking for specific problems, but please let me know if I should modify to improve further).

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    I think this is much easier now than it was around say, 2000. The rise of iOS, Android and Google Docs/Sheets and other web apps have really reduced the MS Stranglehold on office applications and sharing data.
    – ObscureOwl
    Commented Dec 7, 2019 at 11:31
  • 1
    Universities can be somewhat more open about letting individual employees chose their OS- you would never have this choice in most corporate environments. Commented Dec 7, 2019 at 19:15
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    In my experience in STEM departments IT is aware that "one size" does not fit research computers at all.
    – ObscureOwl
    Commented Dec 8, 2019 at 15:40

2 Answers 2


This question might well be closed as off-topic, but here is my experience as a mathematics professor who has used Linux on his primary desktop machine at work (and on my computer at home and on my personal laptop) for 20 years. Before that I ran Solaris on Sun workstations. Before my academic career, I worked as a Unix system administrator in the 1980s, so I had a lot of background.

  1. Your IT department might be unwilling to allow you to run Linux on a university-owned computer and might be unwilling to allow you to connect your personally-owned Linux machine to the campus network.

  2. You may be required to purchase university-owned computers from a particular vendor whose hardware might not work well with Linux.

  3. Your institution might require you to use specific software that only runs on Windows. For example, earlier versions of the widely used Banner ERP system couldn't be used in Linux. I used to have to authorize purchases that were made with my department's purchasing cards using a Windows only software package (actually a web app that required Internet Explorer 6 and wouldn't work with Firefox or Chrome.)

  4. You may have trouble interchanging MS Word Documents or Excel spreadsheets with Windows users (Libreoffice is pretty good but still not perfect.)

  5. You may not be able to use licensed software (such as SAS, MATLAB, etc.) that the university has site licensed for Windows.

  6. Your students and colleagues will probably be using Windows machines and you won't have an environment that perfectly duplicates their setup. This can make it difficult to reproduce problems that they have, even with free software. For example, I recently had an issue using Octave (an open-source MATLAB like language.) My code ran fine in Octave under Linux but failed in Octave under Windows when a colleague used it. This turned out to be due to a bug in the math library that was used on the Windows build of Octave.

  7. Your IT department will almost certainly not provide any support for problems that you might have with your Linux system- you'll be on your own to resolve any issues that come up.

I've always made sure to maintain access to a Windows machine for this few times when I really need it, but in recent years that's been extremely rare. I've got a university-owned Windows laptop that I haven't powered up since July, and I don't miss it. Despite dealing with many of the issues above, I've had a very good experience using Linux and wouldn't consider switching back.

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    As a postdoc in theoretical biology, I've experienced 4 (potential issue with collaborators who don't use latex) and 7 (problem with hooking into uni's decentralised printing system). To add on to 4, you don't get the Adobe suite. Inkscape/gimp can replace illustrator/photoshop but I haven't found a linux replacement for having to sign some digital documents used by my uni (I get around this by dual booting).
    – user49483
    Commented Dec 7, 2019 at 8:37
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    @user49483 I also don't know how to digitally sign things in Linux. Printing is just one of a number of network resources that sometimes cannot be used by machines that are not part of the windows network. Instead of dual booting, I suggest a virtual machine or remote desktop.
    – StrongBad
    Commented Dec 7, 2019 at 13:50
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    Going back and forth between LibreOffice and Word screwed up one of my fellowship applications ... would not recommend. Now I stick to using Word for any document that matters, like paper drafts and grants. Commented Dec 7, 2019 at 22:38
  • @StrongBad Yea I shouldn't have implied that's the reason I dual boot (I do use a virtual machine with W10 for my work desktop but dual boot on my laptop, the latter mainly because of a computer game that needs windows). The printing actually isn't even an issue because I can connect via IP address which is good enough for me (I only lose the ability to print anywhere on campus).
    – user49483
    Commented Dec 7, 2019 at 23:36
  • @Brian Thanks these are very helpful points - I asked mostly about software but issues you mention highlight how far out this can affect interactions and resources (IT, purchasing software, debugging communication, etc). What Linux distribution(s) do you use currently?
    – DirtStats
    Commented Dec 11, 2019 at 16:45

If your course requires the use of computer software, you need to be familiar with the Windows version since that is what your students will probably be using.

Put simply, if the assessment tasks require the use of certain pieces of software, unless you’re teaching a course on the use of Linux and Linux machines are easily available for the students to use through the university, most of the work your students will be doing will be on Windows computers.

If your answer to “how do I do this thing you want us to do for our assignment on Windows” is “I don’t know because I use Linux,” prepare for a number of very frustrated students to give you poor reviews in their teaching feedback forms at the end of semester.

  • Unless you can tell them "the software is available on the Linux terminals in the computer lab".
    – ObscureOwl
    Commented Dec 8, 2019 at 15:42

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