BioLinux
Encyclopedia
BioLinux is a term used in a variety of projects involved in making access to bioinformatics
software on a Linux
platform easier using one or more of the following methods:
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.
is a freely-distributed version of the commercial Red Hat
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
systems. Other distributions such as Mandriva
and SUSE
use RPMs, so these packages may also work on these distributions.
is another very popular Linux distribution
in use in many academic institutions, and some bioinformaticians have made their own software packages available for this distribution in the deb
format.
is one of the less used Linux distributions
. 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
and it has been used as a base for many of the bioinformatics distributions.
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. These include:
Similarly, eBioinformatics provides a Mac OS GUI
for over 300 open source bioinformatics programs.
Gentoo Linux
Gentoo Linux
provides over 50 bioinformatics applications (see packages.gentoo.org and Gentoo Science Overlay) in the form of ebuild
s, which build the applications from source code.
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.
FreeBSD
FreeBSD
is not a Linux distribution, but as it is a version of Unix it is very similar. Its ports
are like Gentoo's ebuilds, and the same caveats apply. However, there are also pre-complied binary packages available. There are over 60 biological sciences applications, and they're listed on the Fresh Ports site.
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 or other Debian-derived installations.
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
software on a Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
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 DVDDVDA DVD is an optical disc storage media format, invented and developed by Philips, Sony, Toshiba, and Panasonic in 1995. DVDs offer higher storage capacity than Compact Discs while having the same dimensions....
/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.
Complete systems
Various complete distributions that integrate bioinformatics software are available, in various stages of development.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. FedoraFedora (operating system)
Fedora is a RPM-based, general purpose collection of software, including an operating system based on the Linux kernel, developed by the community-supported Fedora Project and sponsored by Red Hat...
is a freely-distributed version of the commercial Red Hat
Red Hat
Red Hat, Inc. is an S&P 500 company in the free and open source software sector, and a major Linux distribution vendor. Founded in 1993, Red Hat has its corporate headquarters in Raleigh, North Carolina with satellite offices worldwide....
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
RPM Package Manager
RPM Package Manager is a package management system. The name RPM variously refers to the .rpm file format, files in this format, software packaged in such files, and the package manager itself...
(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
Red Hat Enterprise Linux is a Linux-based operating system developed by Red Hat and targeted toward the commercial market. Red Hat Enterprise Linux is released in server versions for x86, x86-64, Itanium, PowerPC and IBM System z, and desktop versions for x86 and x86-64...
systems. Other distributions such as Mandriva
Mandriva
Mandriva S.A. is a publicly traded Linux and open source software company with its headquarters in Paris, France and development center in Curitiba, Brazil. Mandriva, S.A...
and SUSE
SUSE Linux distributions
SUSE Linux is a computer operating system. It is built on top of the open source Linux kernel and is distributed with system and application software from other open source projects. SUSE Linux is of German origin and mainly developed in Europe. The first version appeared in early 1994, making...
use RPMs, so these packages may also work on these distributions.
- BioRPMs (RedHat and Fedora)
- RPMfind.net (Various RPM-based distributions, indexed by category)
Debian
DebianDebian
Debian is a computer operating system composed of software packages released as free and open source software primarily under the GNU General Public License along with other free software licenses. Debian GNU/Linux, which includes the GNU OS tools and Linux kernel, is a popular and influential...
is another very popular Linux distribution
Linux distribution
A Linux distribution is a member of the family of Unix-like operating systems built on top of the Linux kernel. Such distributions are operating systems including a large collection of software applications such as word processors, spreadsheets, media players, and database applications...
in use in many academic institutions, and some bioinformaticians have made their own software packages available for this distribution in the deb
Deb (file format)
deb is the extension of the Debian software package format and the most often used name for such binary packages. Like the "Deb" part of the term Debian, it originates from the name of Debra, erstwhile girlfriend and now ex-wife of Debian's founder Ian Murdock.Debian packages are also used in...
format.
- Debian Med (Debian contains a lot of medical software internally)
- NEBC Bio-Linux (Non-standard Debian)
Slackware
SlackwareSlackware
Slackware is a free and open source Linux-based operating system. It was one of the earliest operating systems to be built on top of the Linux kernel and is the oldest currently being maintained. Slackware was created by Patrick Volkerding of Slackware Linux, Inc. in 1993...
is one of the less used Linux distributions
Linux distribution
A Linux distribution is a member of the family of Unix-like operating systems built on top of the Linux kernel. Such distributions are operating systems including a large collection of software applications such as word processors, spreadsheets, media players, and database applications...
. 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
Slax is a LiveCD Linux distribution based on Slackware and is currently being developed by Tomáš Matějíček. Packages can be selected in a website where users can build a custom Slax iso image. Slax slogan refers to the software as a "Pocket Operating System"...
and it has been used as a base for many of the bioinformatics distributions.
- BioSLAXBioSLAXBioSLAX is a Live CD/Live DVD/Live USB comprising a suite of more than 300 bioinformatics tools and application suites. It has been released by the of the , National University of Singapore and is bootable from any PC that allows a CD/DVD or USB boot option and runs the compressed Slackware...
Apple/Mac
Many Linux packages are compatible with Mac OS XMac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
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. These include:
Similarly, eBioinformatics provides a Mac OS GUI
Gui
Gui or guee is a generic term to refer to grilled dishes in Korean cuisine. These most commonly have meat or fish as their primary ingredient, but may in some cases also comprise grilled vegetables or other vegetarian ingredients. The term derives from the verb, "gupda" in Korean, which literally...
for over 300 open source bioinformatics programs.
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 (e.g. BioKnoppix).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
Gentoo Linux is a computer operating system built on top of the Linux kernel and based on the Portage package management system. It is distributed as free and open source software. Unlike a conventional software distribution, the user compiles the source code locally according to their chosen...
provides over 50 bioinformatics applications (see packages.gentoo.org and Gentoo Science Overlay) in the form of ebuild
Ebuild
An ebuild is a specialized bash script format created by the Gentoo Linux project for use in its Portage software management system, which automates compilation and installation procedures for software packages....
s, which build the applications from source code.
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.
FreeBSD
FreeBSD
FreeBSD
FreeBSD is a free Unix-like operating system descended from AT&T UNIX via BSD UNIX. Although for legal reasons FreeBSD cannot be called “UNIX”, as the direct descendant of BSD UNIX , FreeBSD’s internals and system APIs are UNIX-compliant...
is not a Linux distribution, but as it is a version of Unix it is very similar. Its ports
Ports collection
Ports collections are the sets of makefiles and patches provided by the BSD-based operating systems, FreeBSD, NetBSD, and OpenBSD, as a simple method of installing software or creating binary packages...
are like Gentoo's ebuilds, and the same caveats apply. However, there are also pre-complied binary packages available. There are over 60 biological sciences applications, and they're listed on the Fresh Ports site.
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 or other Debian-derived installations.
Community building and support systems
Providing support and documentation should be an important part of any BioLinux project, 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.- Bio-Linux BR
- BioLinux Grupo
- NEBC Bio-Linux
- EMBnet.News Two issues (2007) dedicated to Bioinformatics Linux distributions