Ask a newcomer about Linux and they’ll probably mention something about Ubuntu. Someone a little more knowledgeable about Linux will know that there are many flavours, called “distributions” (or “distros”, for short), of Linux. There are over six hundred distributions out there, and they’re all labelled as “Linux”. What makes one distro different from the next, and how do you choose one?

Why are there so many distros?

Strictly speaking, Linux is not an operating system, but rather the kernel of one. However, in most common uses, “Linux” refers to an operating system based on the Linux kernel. Consequently, an operating system that uses the Linux kernel as its kernel can technically be called “Linux”, and these are what distributions are: operating systems that use the Linux kernel.
The main reason for the mass of distributions available is because Linux is freely licensed under the GNU General Public License, version 2 (GPLv2). Since Linux is free software, the following freedoms apply:

• The freedom to run the program as you wish, for any purpose (freedom 0).
• The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this.
• The freedom to redistribute copies so you can help your neighbor (freedom 2).
• The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this.

The ability for people to use Linux for whatever purpose they wish and to change it as desired is perhaps the biggest reason for all the distributions. People take a distribution they like and modify it to suit their purposes; the result is a mind-boggling genesis tree.

What are some examples of Linux distributions?

Some of the most popular distributions are:

• Linux Mint
• Ubuntu
• Debian
• Mageia
• Fedora
• openSUSE
• Arch Linux
• CentOS
• PCLinuxOS
• Slackware Linux
• Android

Yes, Android is a Linux distribution, and this is because Android uses the Linux kernel.

I think it’s safe to say that many, if not most, of the more well-known distributions are ultimately based on or had origins in Debian, Fedora/Red Hat, Mandrake/Mandriva, Slackware, Gentoo, or Arch.

What’s the difference between distributions?

There are two basic elements that define a distribution: the packages it provides and provides initially, and the community it attracts. Encompassing all that is the distro’s core philosophy.

Software in Linux is provided through packages, which are supplied through the distribution’s software repositories. The distro’s goal and philosophy will dictate what packages will be put in the repositories and how frequently they will update. For example, Debian only includes free software in its supported repositories and updates very infrequently. In contrast, Arch Linux includes almost everything because its philosophy is to leave it up to the user to decide, and the packages are updated as often as the software updates.
More specifically, another key difference between distros is the list of packages that are included in the base installation. Different distros ship specific packages to provide different default desktop environments like GNOME, KDE, XFCE, or LXDE, as well as its own package manager and other bundled software. The number of packages can range from the bare minimum (e.g. LFS, Gentoo, Arch) to very many (e.g. Ubuntu, Mint, openSUSE).

Because of its philosophy, the distro will naturally cater to a certain community, whether it be beginners, experts, free software advocates, or even Satanists. This community sets the overall mood and friendliness of the distro’s forums, which can sometimes deter those who don’t “fit” in the community. Furthermore, I would consider the quality and quantity of documentation as part of the community; some distros have hard to find or even almost no documentation, and some have really well-written documentation.

Which distribution should I use?

This is a tough one to answer; the answer is always something along the lines of “it depends”. The distribution you should use depends on your skill level, your use cases, and any restrictions you might impose. Beginners are often directed to Ubuntu or Linux Mint, and advanced users to Arch Linux or Gentoo. Many servers run Debian or Fedora for their reputation for being very stable. Those with older hardware may go with something like Puppy Linux.

To pick out a distro that’s right for you, answer these questions:

• Who will be using it?
• What will it be installed on? / How powerful is the computer?
• What will it be used for? / Why do you want to install it?
• How often will you be using it?
• How much time and effort are you willing to put into maintaining it?
• How skilled are you with computers? How quickly do you learn new technical things?

When you’ve answered those questions, do a search for a distribution using your answers as keywords. You can even try an online distro chooser (do a search for one) that will match you with a distribution based on your answers to its questionnaire. Look at the distro chooser as an aid, not as a final decision; for example, I always get matched with Gentoo, but I prefer Arch. Don’t forget that you can ask friends with Linux experience, too. Once you find a distribution that appeals to you, do some more research on it to make sure that it and its community will suit you and how to install it.

The best way to determine if a distribution is right for you is to try it out. Many, if not most, distros come as in “LiveCD/LiveDVD/LiveUSB” form, which lets you run the distro off the disc/USB drive without needing to install it first. After playing around with it and decide that you like it enough to install it, there’s often an option to install it right from the Live environment. If you’re not comfortable with installing on your drive right away, you can install it in a virtual machine first to get familiar with the process (virtual machines are outside the scope of this post, but I recommend VirtualBox).

Before installing to your disk, remember to back up your data and have your recovery media handy: in the case that anything goes wrong, you’ll have something you can go back to.

There are many distributions out there to choose from and they all exist to solve a problem or to cater to a certain community. The difference between them boils down to the software they include and the communities they attract. Choosing one is a matter of identifying your needs and finding one whose philosophy, workflow and community appeal to you.

Choosing a Linux distribution for bioinformatics analysis

Choosing a Linux distribution for bioinformatics analysis is a crucial decision that can impact your workflow, software compatibility, and overall productivity. Several factors should be considered when selecting a distribution, including stability, software availability, and user preference.

1. Stability: Stability is a critical factor in bioinformatics, where data integrity and reliability are paramount. A stable Linux distribution ensures that your system operates smoothly without unexpected crashes or errors, which is essential when working with large datasets and complex analysis pipelines.
2. Software Availability: The availability of bioinformatics software and tools is another important consideration. A good Linux distribution should have a robust package management system and a wide range of software packages tailored for bioinformatics analysis. This includes tools for sequence alignment, genome assembly, gene prediction, and data visualization.
3. User Preference: User preference plays a significant role in choosing a Linux distribution. Some users prefer distributions with a minimalistic, lightweight desktop environment, while others prefer distributions with a more feature-rich desktop environment. It’s essential to choose a distribution that aligns with your preferences and workflow.

Ubuntu LTS (Long-Term Support)

Ubuntu LTS (Long-Term Support) versions are a specific release variant of the Ubuntu Linux distribution that are designed for stability and long-term maintenance. These versions are typically released every two years and receive updates and support for five years, making them ideal for users who prioritize stability and consistency over having the latest features.

One of the key reasons why Ubuntu LTS versions are well-suited for bioinformatics analysis is their large user base and extensive software repositories. Ubuntu is one of the most popular Linux distributions, which means that there is a vast community of users and developers who contribute to its ecosystem. As a result, Ubuntu LTS versions come with a wide range of software packages, including many bioinformatics tools and libraries.

The availability of bioinformatics software in Ubuntu’s repositories is crucial for bioinformatics researchers and analysts. It means that you can easily install and manage bioinformatics tools using Ubuntu’s package management system, which simplifies the setup and maintenance of your bioinformatics analysis environment.

Furthermore, Ubuntu LTS versions are known for their stability. The Ubuntu development team focuses on rigorous testing and quality assurance processes to ensure that LTS releases are reliable and free from major bugs. This stability is essential for bioinformatics analysis, where data integrity and consistency are critical.

In summary, Ubuntu LTS versions are well-suited for bioinformatics analysis due to their stability, long-term support, large user base, and extensive software repositories. If you prioritize stability and reliability in your bioinformatics work, Ubuntu LTS can be an excellent choice for your desktop environment.

Debian

Debian is a Unix-like operating system and one of the oldest Linux distributions, known for its stability, reliability, and strict adherence to the principles of free and open-source software. These characteristics make Debian an excellent choice for bioinformatics, where reliability and data integrity are crucial.

One of Debian’s key strengths is its package management system, which allows users to easily install, update, and manage software packages. Debian has a vast selection of software packages available through its repositories, which are maintained by the Debian project and its community. These repositories include many bioinformatics tools and libraries, making it easy for bioinformatics researchers and analysts to access the software they need for their work.

While Debian prioritizes stability and reliability, this can sometimes come at the expense of having the latest versions of software. Debian’s release cycle is known for being conservative, with new stable releases typically occurring every two years. As a result, the versions of software available in Debian’s repositories may not always be the most up-to-date. However, Debian does provide security updates and bug fixes for its stable releases, ensuring that the software remains stable and secure over time.

In addition to its stability and reliability, Debian is also known for its strong commitment to free and open-source software principles. This means that all software included in Debian’s repositories is free to use, modify, and distribute, which is important for many bioinformatics researchers and analysts who value open access to software and data.

In summary, Debian is renowned for its stability, reliability, and commitment to free and open-source software, making it an excellent choice for bioinformatics. While it may not always have the latest versions of software, Debian provides a solid and dependable platform for bioinformatics work.

CentOS

CentOS is a Linux distribution that is known for its stability, reliability, and long-term support. It is a community-supported rebuild of Red Hat Enterprise Linux (RHEL), which means that it is based on the same source code as RHEL but is maintained by the CentOS community rather than by Red Hat. CentOS aims to provide a free and open-source alternative to RHEL, with the same level of stability and compatibility.

One of the key reasons why CentOS is popular in scientific computing and bioinformatics is its compatibility with RHEL. Many bioinformatics software packages are developed and tested on RHEL, so CentOS provides a stable and reliable platform for running these software packages without the cost of RHEL licenses. This compatibility also extends to hardware, as CentOS supports a wide range of hardware platforms commonly used in bioinformatics.

Another advantage of CentOS is its long-term support. Like RHEL, CentOS releases are supported for up to 10 years, which is longer than the support periods offered by many other Linux distributions. This long-term support is important in bioinformatics, where data analysis pipelines and software environments need to be stable and consistent over long periods of time.

CentOS is also known for its security features, with regular security updates and patches provided by the CentOS community. This ensures that CentOS remains a secure platform for bioinformatics work, protecting sensitive data and analysis results from security vulnerabilities.

In summary, CentOS is a community-supported rebuild of Red Hat Enterprise Linux known for its stability, long-term support, and compatibility with RHEL. It is widely used in scientific computing and bioinformatics due to its reliability and security features, making it an excellent choice for bioinformatics researchers and analysts who require a stable and dependable platform for their work.

Fedora

Fedora is a Linux distribution sponsored by Red Hat and known for its cutting-edge features and up-to-date software. It serves as a testing ground for technologies that may eventually be incorporated into Red Hat Enterprise Linux (RHEL), making it an attractive choice for users who want access to the latest developments in the Linux ecosystem.

One of the key advantages of Fedora for bioinformatics analysis is its up-to-date software and features. Fedora typically includes the latest versions of software packages, including bioinformatics tools and libraries. This can be beneficial for bioinformatics researchers and analysts who require access to the latest features and improvements in bioinformatics software.

However, Fedora’s rapid release cycle may result in occasional stability issues. Because Fedora focuses on delivering new features and technologies quickly, stability can sometimes be compromised. This can be a concern for bioinformatics researchers and analysts who require a stable and reliable platform for their work.

Despite these potential stability issues, Fedora offers several advantages for bioinformatics analysis. It provides a rich set of software packages through its repositories, making it easy to install and manage bioinformatics tools. Additionally, Fedora benefits from the support and expertise of the Red Hat community, ensuring that users have access to resources and assistance when needed.

In summary, Fedora is a cutting-edge Linux distribution sponsored by Red Hat that offers up-to-date software and features, making it an attractive choice for bioinformatics analysis. However, its rapid release cycle may result in occasional stability issues, which should be considered when choosing a distribution for bioinformatics work.

OpenSUSE Leap

OpenSUSE Leap is a Linux distribution known for its stability, ease of use, and community-driven development model. It is a version of OpenSUSE that follows a regular release cycle and is designed to be stable and reliable, making it well-suited for desktop use in bioinformatics.

One of the key strengths of OpenSUSE Leap is its stability. The Leap release cycle is based on the development cycle of SUSE Linux Enterprise (SLE), which is known for its stability and reliability in enterprise environments. This means that OpenSUSE Leap benefits from the rigorous testing and quality assurance processes of SLE, ensuring that it provides a stable platform for bioinformatics analysis.

In addition to stability, OpenSUSE Leap is known for its ease of use. It features the YaST (Yet another Setup Tool) configuration tool, which provides a graphical interface for managing system settings and installing software. This makes it easy for users to set up and configure their bioinformatics analysis environment without needing to use the command line extensively.

OpenSUSE Leap also offers a good selection of software packages through its repositories, including many bioinformatics tools and libraries. This makes it easy for bioinformatics researchers and analysts to access the software they need for their work, without having to search for or manually install software packages.

Overall, OpenSUSE Leap is a stable, easy-to-use Linux distribution that offers a good selection of software packages, making it well-suited for desktop use in bioinformatics. Its stability, ease of use, and community-driven development model make it a solid choice for bioinformatics researchers and analysts who require a reliable platform for their work.