Why All Bioscientists Should Use Linux

Published August 20, 2009

Posted in: Organization and Productivity

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: https://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!

Discover some of the wonderful free software that is available for biologists using Linux.

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

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Written by Peter Blazso

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18 Comments

Rick Davis on August 25, 2009 at 8:03 pm

It is great to see GNU/Linux get some good press for bioscientists! Although it takes some tweaking to get used to, Linux offers more choice and freedom in your computing. Want to try bioinformatics? Just install the software at the click of a button. Video editing, desktop publishing, webpage design? the same. All free of charge.

As far as word processors go, I’m a happy user of OpenOffice. I think the newest releases are stable and have all of the features I need to trust it with large, complex documents. It also works well with Zotero for making bibliographies. It also uses an open XML format to save your documents, so you’ll always be able to open them in the future. You will get no such promises from Coral.

Alternative word processors available for linux include ABIword, which is a small, fast processor. The great LyX which incorporates LaTeX into the processor allowing awesome looking technical documents without having to use a “formula” program. Kword is being completely re-written at the moment but promises to have some very exciting features like extensions that are easy to write and a clean codebase that will allow new features at a fast pace. Again, all free of charge to try and decide which to use.

Jon Galt on August 23, 2009 at 4:10 am

OK, so here’s the stopper for me: there is no half-decent word processor for Linux. OpenOffice is as close as it gets, but they seem persistent in making their word processor work like Word–about as bad a model as there could be. Yes, you can get WordPerfect for Linux, but it’s just ported from Windows and requires Wine, so it’s not pretty.

Given WP’s vanishingly small market share and the lack of outcry over the horrors of Word, one has to wonder if writing has gone the way of the dinosaur. But I for one am still dependent enough on a functional word processor to be unable to commit to full-time Linux.

Peter on August 23, 2009 at 9:13 am
Jon:
What does “functional” mean to you in case of a word processor? Which word processor do you use currently? What does OpenOffice lack that you need? I really want to learn from your experience. Have you tried other alternatives like KLyx, KWord or Abiword? Also nice commercial office suites exist for Linux like IBM Lotus Symphony or SoftMaker Office. Do you know them?
Log in to Reply

David Crotty on August 22, 2009 at 8:55 pm

Hey, I’m a longtime Mac user, I know where you’re coming from. That said, “immune” is an overstatement for any OS. “More immune”, “better security from the ground up”, sure, great, no problem, but telling people they will never have any security issues goes too far.

Peter on August 22, 2009 at 11:06 pm
David:
I wanted to denote that people do not need to use additional anti-virus/trojan/etc solutions besides regular updates. I modified the text accordingly. Thanks for your comments!
Where do you think I am coming from… ? 😉
Log in to Reply

Aaron Stephan on August 21, 2009 at 8:32 pm

Thank you for writing this article! I’ve been running Ubuntu Linux on my computer for the past 3 years, and use it almost exclusively during my Ph.D research in neuroscience. Because, in my opinion, Linux isn’t as polished as Windows/Mac OSX, I’ve learned to troubleshoot a lot. Because the software is free, there is nobody to get mad at. Instead, I get any help I need from the vast community of open source developers and users. I’ve even learned to contribute some of my own fixes! I feel like I’ve re-established dominance over the computer, and as such, I can better use it to solve the problem at hand. I even find myself to be a smarter user of Windows and Macs due to my experience in Linux.

David Crotty on August 21, 2009 at 6:51 pm

Felipe, the key word here is “immune”. No system is completely immune to viruses, and it’s misleading to suggest otherwise.

Peter on August 21, 2009 at 9:42 pm
David:
There is no system that is perfectly secure. Neither is Linux. Security threats do exist on these systems as well, but malicious algorithms can do harm only when the system is vulnerable. Any malware (including viruses, trojans, worms, etc.) FIRST exploits a security vulnerability (security hole) and THEN does nasty things. If you “patch” that hole in time then you will be protected against that threat (and probably numerous others as well) and your system will be “immune” and you won’t need costly anti-malware solutions. If you or the OS vendor leaves that hole “unpatched” for a long time (because you do not care or the vendors do not know about it, they don’t have the developer capacity to deal with security issues or intentionally keep it secret) then sooner or later it will be exploited. Linux is open-source so everything is open, known, constantly developed and peer-reviewed by thousands (or more). If somebody finds a hole, usually announces it and a patch can be made and spread quickly. Most of the times before it can be exploited. This is one of the reasons why most of the big Linux distributions have very good security records. It means that they have low number of critical + unpatched vulnerabilities and short response times to emerging security issues compared to the closed-source, proprietary OS-s. You can check here some current security statistics of Ubuntu Linux 9.04: https://secunia.com/advisories/product/21851/.
These are the things why I used the word “immune” but this is true only when you (have your system) update regularly. However, there is no need to use antivirus software, waste money and precious CPU time. Updating/patching and proper configuration should be enough and your system becomes “immune” (to most of the known threats).
Log in to Reply

Rick Davis on August 25, 2009 at 8:03 pm
It is great to see GNU/Linux get some good press for bioscientists! Although it takes some tweaking to get used to, Linux offers more choice and freedom in your computing. Want to try bioinformatics? Just install the software at the click of a button. Video editing, desktop publishing, webpage design? the same. All free of charge.
As far as word processors go, I’m a happy user of OpenOffice. I think the newest releases are stable and have all of the features I need to trust it with large, complex documents. It also works well with Zotero for making bibliographies. It also uses an open XML format to save your documents, so you’ll always be able to open them in the future. You will get no such promises from Coral.
Alternative word processors available for linux include ABIword, which is a small, fast processor. The great LyX which incorporates LaTeX into the processor allowing awesome looking technical documents without having to use a “formula” program. Kword is being completely re-written at the moment but promises to have some very exciting features like extensions that are easy to write and a clean codebase that will allow new features at a fast pace. Again, all free of charge to try and decide which to use.
Log in to Reply
Jon Galt on August 23, 2009 at 4:10 am
OK, so here’s the stopper for me: there is no half-decent word processor for Linux. OpenOffice is as close as it gets, but they seem persistent in making their word processor work like Word–about as bad a model as there could be. Yes, you can get WordPerfect for Linux, but it’s just ported from Windows and requires Wine, so it’s not pretty.
Given WP’s vanishingly small market share and the lack of outcry over the horrors of Word, one has to wonder if writing has gone the way of the dinosaur. But I for one am still dependent enough on a functional word processor to be unable to commit to full-time Linux.
Log in to Reply
- Peter on August 23, 2009 at 9:13 am
  Jon:
  What does “functional” mean to you in case of a word processor? Which word processor do you use currently? What does OpenOffice lack that you need? I really want to learn from your experience. Have you tried other alternatives like KLyx, KWord or Abiword? Also nice commercial office suites exist for Linux like IBM Lotus Symphony or SoftMaker Office. Do you know them?
  Log in to Reply
David Crotty on August 22, 2009 at 8:55 pm
Hey, I’m a longtime Mac user, I know where you’re coming from. That said, “immune” is an overstatement for any OS. “More immune”, “better security from the ground up”, sure, great, no problem, but telling people they will never have any security issues goes too far.
Log in to Reply
- Peter on August 22, 2009 at 11:06 pm
  David:
  I wanted to denote that people do not need to use additional anti-virus/trojan/etc solutions besides regular updates. I modified the text accordingly. Thanks for your comments!
  Where do you think I am coming from… ? 😉
  Log in to Reply
Aaron Stephan on August 21, 2009 at 8:32 pm
Thank you for writing this article! I’ve been running Ubuntu Linux on my computer for the past 3 years, and use it almost exclusively during my Ph.D research in neuroscience. Because, in my opinion, Linux isn’t as polished as Windows/Mac OSX, I’ve learned to troubleshoot a lot. Because the software is free, there is nobody to get mad at. Instead, I get any help I need from the vast community of open source developers and users. I’ve even learned to contribute some of my own fixes! I feel like I’ve re-established dominance over the computer, and as such, I can better use it to solve the problem at hand. I even find myself to be a smarter user of Windows and Macs due to my experience in Linux.
Log in to Reply
David Crotty on August 21, 2009 at 6:51 pm
Felipe, the key word here is “immune”. No system is completely immune to viruses, and it’s misleading to suggest otherwise.
Log in to Reply
- Peter on August 21, 2009 at 9:42 pm
  David:
  There is no system that is perfectly secure. Neither is Linux. Security threats do exist on these systems as well, but malicious algorithms can do harm only when the system is vulnerable. Any malware (including viruses, trojans, worms, etc.) FIRST exploits a security vulnerability (security hole) and THEN does nasty things. If you “patch” that hole in time then you will be protected against that threat (and probably numerous others as well) and your system will be “immune” and you won’t need costly anti-malware solutions. If you or the OS vendor leaves that hole “unpatched” for a long time (because you do not care or the vendors do not know about it, they don’t have the developer capacity to deal with security issues or intentionally keep it secret) then sooner or later it will be exploited. Linux is open-source so everything is open, known, constantly developed and peer-reviewed by thousands (or more). If somebody finds a hole, usually announces it and a patch can be made and spread quickly. Most of the times before it can be exploited. This is one of the reasons why most of the big Linux distributions have very good security records. It means that they have low number of critical + unpatched vulnerabilities and short response times to emerging security issues compared to the closed-source, proprietary OS-s. You can check here some current security statistics of Ubuntu Linux 9.04: https://secunia.com/advisories/product/21851/.
  These are the things why I used the word “immune” but this is true only when you (have your system) update regularly. However, there is no need to use antivirus software, waste money and precious CPU time. Updating/patching and proper configuration should be enough and your system becomes “immune” (to most of the known threats).
  Log in to Reply

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