BioLinux is a term used in a variety of projects involved in making access to

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

software Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

on a

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

platform easier using one or more of the following methods: * Provision of complete systems * Provision of bioinformatics software repositories * Addition of bioinformatics packages to standard distributions * Live

DVD The DVD (common abbreviation for Digital Video Disc or Digital Versatile Disc) is a digital optical disc data storage format. It was invented and developed in 1995 and first released on November 1, 1996, in Japan. The medium can store any kin ...

/ CDs with bioinformatics software added * Community building and support systems There are now various projects with similar aims, on both Linux systems and other Unices, and a selection of these are given below. There is also an overview in the Canadian Bioinformatics Helpdesk Newsletter that details some of the Linux-based projects.

Package repositories

Apple/Mac

Many Linux packages are compatible with

Mac OS X macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac (computer), Mac computers. Within the market of ...

and there are several projects which attempt to make it easy to install selected Linux packages (including bioinformatics software) on a computer running Mac OS X. (source?)

BioArchLinux

BioArchLinux repository
contain more than 3,770 packages for Arch Linux and Arch Linux based distribution.

Debian

Debian Debian (), also known as Debian GNU/Linux, is a Linux distribution composed of free and open-source software, developed by the community-supported Debian Project, which was established by Ian Murdock on August 16, 1993. The first version of D ...

is another very popular

Linux distribution A Linux distribution (often abbreviated as distro) is an operating system made from a software collection that includes the Linux kernel and, often, a package management system. Linux users usually obtain their operating system by downloading one ...

in use in many academic institutions, and some bioinformaticians have made their own software packages available for this distribution in the deb format.

Red Hat

Package repositories are generally specific to the distribution of Linux the bioinformatician is using. A number of Linux variants are prevalent in bioinformatics work.

Fedora A fedora () is a hat with a soft brim and indented crown.Kilgour, Ruth Edwards (1958). ''A Pageant of Hats Ancient and Modern''. R. M. McBride Company. It is typically creased lengthwise down the crown and "pinched" near the front on both sides ...

is a freely-distributed version of the commercial

Red Hat Red Hat, Inc. is an American software company that provides open source software products to enterprises. Founded in 1993, Red Hat has its corporate headquarters in Raleigh, North Carolina, with other offices worldwide. Red Hat has become ass ...

system. Red Hat is widely used in the corporate world as they offer commercial support and training packages. Fedora Core is a community supported derivative of Red Hat and is popular amongst those who like Red Hat's system but don't require commercial support. Many users of bioinformatics applications have produced RPMs (Red Hat's package format) designed to work with Fedora, which you can potentially also install on

Red Hat Enterprise Linux Red Hat Enterprise Linux (RHEL) is a commercial open-source Linux distribution developed by Red Hat for the commercial market. Red Hat Enterprise Linux is released in server versions for x86-64, Power ISA, ARM64, and IBM Z and a desktop version ...

systems. Other distributions such as

Mandriva Mandriva S.A. was a public software company specializing in Linux and open-source software. Its corporate headquarters was in Paris, and it had development centers in Metz, France and Curitiba, Brazil. Mandriva, S.A. was the developer and mainta ...

and

SUSE SUSE ( , ) is a German-based multinational open-source software company that develops and sells Linux products to business customers. Founded in 1992, it was the first company to market Linux for enterprise. It is the developer of SUSE Linux Ent ...

use RPMs, so these packages may also work on these distributions.

Slackware

Slackware Slackware is a Linux distribution created by Patrick Volkerding in 1993. Originally based on Softlanding Linux System, Slackware has been the basis for many other Linux distributions, most notably the first versions of SUSE Linux distributions ...

is one of the less used

s. It is popular with those who have better knowledge of the Linux operating system and who prefer the command line over the various GUIs available. Packages are in the tgz or tgx format. The most widely known live distribution based on Slackware is

Slax Slax is a LiveCD Linux distribution developed by Tomáš Matějíček and based on upstream customizable Linux distributions. Packages can be added by apt package manager or can be prepared as modules. The tagline for Slax refers to itself as " ...

and it has been used as a base for many of the bioinformatics distributions. * BioSLAX

Live DVDs/CDs

Live DVDs or CDs are not an ideal way to provide bioinformatics computing, as they run from a CD/DVD drive. This means they are slower than a traditional hard disk installation and have limited ability to be configured. However, they can be suitable for providing ''ad hoc'' solutions where no other Linux access is available, and may even be used as the basis for a Linux installation.

Standard distributions with good bioinformatics support

In general, Linux distributions have a wide range of official packages available, but this does not usually include much in the way of scientific support. There are exceptions, such as those detailed below. ; Gentoo Linux

Gentoo Linux Gentoo Linux (pronounced ) is a Linux distribution built using the Portage package management system. Unlike a binary software distribution, the source code is compiled locally according to the user's preferences and is often optimized for the ...

provides over 156 bioinformatics applications (se
Gentoo sci-biology herd in the main tree
in the form of

ebuild Portage is a package management system originally created for and used by Gentoo Linux and also by ChromeOS, Calculate, Sabayon, and Funtoo Linux among others. Portage is based on the concept of ports collections. Gentoo is sometimes referred to ...

s, which build the applications from source code. Additional 315 packages are i
Gentoo science overlay
(for testing). Although a very flexible system with excellent community support, the requirement to install from source means that Gentoo systems are often slow to install, and require considerable maintenance. It is possible to reduce some of the compilation time by using a central server to generate binary packages. On the other hand, you can fine tune all to run at the highest speed utilizing the best of your processor (for example to actually use SSE and AVX and AVX2 CPU instructions). Binary-based distro's usually provide binaries using only i686 or even just i386 instruction sets. ; FreeBSD

FreeBSD FreeBSD is a free and open-source Unix-like operating system descended from the Berkeley Software Distribution (BSD), which was based on Research Unix. The first version of FreeBSD was released in 1993. In 2005, FreeBSD was the most popular ...

is not a Linux distribution, but a version of

Unix Unix (; trademarked as UNIX) is a family of multitasking, multiuser computer operating systems that derive from the original AT&T Unix, whose development started in 1969 at the Bell Labs research center by Ken Thompson, Dennis Ritchie, and ot ...

that it is very similar. Its

ports A port is a maritime facility comprising one or more wharves or loading areas, where ships load and discharge cargo and passengers. Although usually situated on a sea coast or estuary, ports can also be found far inland, such as Ham ...

are analogous Gentoo's ebuilds. However, the project continuously builds pre-compiled binary packages for Tier-1 platforms such as

x86 x86 (also known as 80x86 or the 8086 family) is a family of complex instruction set computer (CISC) instruction set architectures initially developed by Intel based on the Intel 8086 microprocessor and its 8088 variant. The 8086 was introd ...

and

ARM In human anatomy, the arm refers to the upper limb in common usage, although academically the term specifically means the upper arm between the glenohumeral joint (shoulder joint) and the elbow joint. The distal part of the upper limb between the ...

. Users can also choose to build and install any port from source in order to enable non-portable optimizations or other build options. The build-from-source option also allows the ports system to automate installation of software with a license that does not permit redistribution. The ports collection contains over 31,000 ports, of which over 2,200 are in scientific categories, and over 240 are biology-related. New ports and updates are listed on the Fresh Ports site. ; pkgsrc The

pkgsrc pkgsrc (''package source'') is a package management system for Unix-like operating systems. It was forked from the FreeBSD ports collection in 1997 as the primary package management system for NetBSD. Since then it has evolved independently; in 19 ...

package manager, originally forked from

FreeBSD ports The FreeBSD Ports collection is a package management system for the FreeBSD operating system, providing an easy and consistent way of installing software packages. As of February 2020, there are over 38,487 ports available in the collection. It has ...

, is maintained by the

NetBSD NetBSD is a free and open-source Unix operating system based on the Berkeley Software Distribution (BSD). It was the first open-source BSD descendant officially released after 386BSD was forked. It continues to be actively developed and is a ...

project, but aims to support all

POSIX The Portable Operating System Interface (POSIX) is a family of standards specified by the IEEE Computer Society for maintaining compatibility between operating systems. POSIX defines both the system- and user-level application programming interf ...

-compatible operating systems. It is well-tested on

, many

distributions,

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and lapt ...

, and

SunOS SunOS is a Unix-branded operating system developed by Sun Microsystems for their workstation and server computer systems. The ''SunOS'' name is usually only used to refer to versions 1.0 to 4.1.4, which were based on BSD, while versions 5.0 and l ...

derivatives. Like FreeBSD ports, pre-compiled binary packages are maintained for some platforms. Packages can be built from source on any platform, or if additional optimizations or options are desired. The pkgsrc collection contains over 19,000 packages, of which nearly 800 are in scientific categories, and over 60 are biology-related. ; Debian There are more than a hundred bioinformatics packages provided as part of the standard Debian installation. NEBC Bio-Linux packages can also be installed on a standard Debian system as long as the bio-linux-base package is also installed. This creates a /usr/local/bioinf directory where our other packages install their software. Debian packages may also work on

Ubuntu Linux Ubuntu ( ) is a Linux distribution based on Debian and composed mostly of free and open-source software. Ubuntu is officially released in three editions: ''Desktop'', '' Server'', and ''Core'' for Internet of things devices and robots. All ...

or other Debian-derived installations.

Community building and support systems

Providing support and documentation should be an important part of any BioLinux project, so that scientists who are not IT specialists may quickly find answers to their specific problems. Support forums or mailing lists are also useful to disseminate knowledge within the research community. Some of these resources are linked to here.

References

{{Free healthcare software Bioinformatics software Linux Computational science