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Why All Bioscientists Should Use Linux

Why All Bioscientists Should Use Linux

A couple of weeks ago, Nick tried to convince us that we should all be using Macs. But why would you want to use a Mac (or a PC) when you could have an operating system that:

  • Is free
  • Does not slow down after a while and limit your productivity
  • Does not need extra antivirus protection besides regular updates
  • Has tens of thousands of programs available for free
  • Has a vigorous community who are willing to help you solve any problems you might have?

That operating system is Linux. And I think that it is high time that more bioscientists got to know Linux so I have written this article to help YOU do so.

Linux is not (just) for computer geeks

You have probably heard of Linux. And you might think that it is complicated stuff, reserved for the bioinformatics geeks down the corridor. But this is no longer true.

Since emerging from a “garage project” run by Finnish software developer Linus Torvalds, Linux has benefited from the efforts of thousands (or tens of thousands) of developers who have built it into an extremely powerful operating system with a rich collection of free software to fulfill any requirement you might have.

Best of all it is a free, open source and community supported operating system that can be run right on the computer you are using now, with no need to remove your favorite operating system (be it Windows or Mac).

And before you ask if it is any good, what do you think most of the world’s top supercomputers run: OSX, Windows or Linux? The answer is here!

Know your distros

You don’t have to go to a computer shop to get Linux. It is available for free download from various websites in the form of distributions (or “distros”).

A variety of distros are available and the differences between them are in the types of software that comes packaged with the operating system. Many are specialized for specific tasks like graphic design, sound mixing/editing or performing scientific work (e.g. calculations or DNA alignments). You can find more information about distros here.

I recommend you try Linux out and see if it is better for you than the commercial operating system you are using now. I think you will be pleasantly surprised.

But where do you start? Here’s where:

Explore the power of Linux on your current machine without changing a thing

The easiest way of exploring Linux is to pick and download a “live” CD/DVD image, which can be burned onto a CD or DVD, inserted into your drive and after a restart you’ll have a basic, fully set up and working Linux environment without any alterations made to your computer.

And don’t worry, if you remove the disc from your drive and restart the computer, your old Windows or Mac OS will boot up as normal.

For first timers I’d recommend Ubuntu because this distro is compiled to be easy and convenient to use. But if you are feeling adventurous, there are many other examples of “live” distros here .

But be warned the live CD/DVD approach will not show you the full power of Linux. Everything will be a bit slower because it has to be loaded and unpacked on-the-fly from a slow optical disk!

Installing Ubuntu Linux on your current machine

If you like what you see, you can then install Linux on your hard drive very easily. Here’s the official guide on how to get set up an up-to-date Ubuntu system.

For the impatient here is what you need to do:

1. Make a backup!

Whenever you are delving into the workings of your computer you should make a full backup of your hard drive. Better safe than sorry.

2. Download and start the installer
Most distros have very beginner-friendly installer, so you do not have to worry about this process at all. Ubuntu has such an installer so, again I’d recommend it for your first Linux experience.

Download the installer and burn it onto a CD or DVD. Then you will be able to start the installer by double-clicking on its desktop icon.

3. Resize your hard disk

Most likely you will set up Linux as a second operating system. In this case you’ll need to have at least 5-6 GBs of free space on your hard drive, which needs to be partitioned off from the rest of your drive. This can be easily done on-the-fly during the installation process.

A standard Ubuntu system needs at least 5-6 GBs of free space where you can create the Linux specific partition(s). It is best to have at least two partitions:

  • A 5 GB ext3 partition. This should have “/” as the mount point. Don’t worry — all will become clear during the installation.
  • A 1 GB  linux swap partition. This acts as the scratch disk, where Linux can use disk space as “virtual memory”. More information on partitioning, filesystems and mount points can be found here.

4. Choose your software

You can get all of the basics like a web browser, email clients, word processors, spreadsheets and media players by simply accepting (1 click!) the pre-selected, default set of to-be-installed packages from a huge list of available software.

If you need to have other programs on your computer than the default ones you can certainly select them in the installer as an option. As I mentioned earlier, there are a great number of bio-specific software packages out there that do great things, and they are all FREE.

There are too many to talk about here, so they will be the subject of our next article…. stay tuned!

5. If you ever need help, no problem.

If you have any problem you can even turn to the comprehensive online documentation and user forums for help. Since Linux and most of the programs built for it are open source which means that the core operating system and most of the utilities were born and brought up in a highly collaborative and open community so you should be able to find an answer to even the most difficult question.

As a reference you may want to bookmark this page: http://www.linux.org. If you like newsgroups check this list. Each distro usually has its own website where you can find documentation, help and user forums.

For Ubuntu users there is an enormous, separate site made only for user discussions. You can find it here. If you prefer books, a vast amount of literature exists on the subject, just check an online bookstore! And if you have a very specific problem (on Linux or anything else for that matter) don’t be afraid to use your favorite web search engine… it will help you a lot!

Are you brave enough to try out Linux? Do you have any questions before you get started? Talk to us in the comments….

18 Comments

  1. Felipe on August 21, 2009 at 6:45 pm

    Well, I use both MacOS X and Linux, and Linux is a must-try. Anyway, you should warn: it is not Windows; the user interface and the working dynamics are not worse, are different. Thus, before trying Linux, you must not expect to start using the system like you did on Windows. The same applies with MacOS X.

    And about virus, if we talk about the classical Windows virus, there are not virus for Linux/MacOS X. Yes, there are malware, but the kind of blight that started attacking MS-DOS, then Windows, it is not possible in Unix-like systems. You can get malware in your ‘X machine, but is much more easier to avoid it. Said after 10 years working with Linux and 6 with MacOS X… no antivirus, no virus, no reinstalls because of malware/weird system behavior.

  2. Andor Kiss on August 21, 2009 at 6:42 pm

    Hi Peter,

    In needing to do FPC Contig Analysis during my PhD I had to use Linux to make use of the free software that came out of the Human Genome Project. After dual booting with Ubuntu Linux for about six months and I mad the plunge to Ubuntu full time. I haven’t looked back. That was three years ago.

    Linux (Ubuntu) is faster, easier, better, less headaches and just simpler to use, and its free and open source (meaning it can be de-bugged much faster).

    – AK

  3. Ann Loraine on August 21, 2009 at 5:38 pm

    Many bioinformatics programs have pre-compiled Windows and Mac OS versions available and ready to install. R, Integrated Genome Browser, Bioconductor, Perl, Python, and many others all run pretty well on diverse operating systems. Don’t risk losing a few days of your valuable time installing a new OS on your computer unless you have a good reason. Or a lot of free time to kill. However, if you are running a Web site or Web service, your life will be a thousand times easier if you run a Unix OS on your server. Good luck all!

    • Peter on August 22, 2009 at 9:02 pm

      Ann:
      Thanks for giving examples of cross-platform software! Of course you don’t have to use Linux. It is an alternative but in case of these programs you can be sure that there will be no data compatibility or conversion problems with others who happen to use Linux.

  4. David Crotty on August 21, 2009 at 2:58 pm

    —Is immune to viruses—

    Wow, that’s good to know, and will certainly come as a surprise to all those out there creating malware and viruses for Linux:
    http://www.internetnews.com/dev-news/article.php/3601946

  5. MadGenius on August 21, 2009 at 10:51 am

    hurrah! more linux love from BSB please.

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