BioLinux

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:

• Provision of complete systems
• Provision of bioinformatics software repositories
• Addition of bioinformatics packages to standard distributions
• Live DVD/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.

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Complete systems

Various complete distributions that integrate bioinformatics software are available, in various stages of development.

• BioBrew
• BioLand
• BioLinuxBR
• Debian-Med
• NEBC Bio-Linux

Package repositories

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 Core 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.

Debian GNU/Linux is another very popular system in use in many academic instututions, and some bioinformaticians have made their own software packages available for this distribution in the deb format.

Though not as widely used as Linux within the scientific community, Mac OS X is gaining in popularity with scientists due to combining an excellent desktop environment with an underlying Unix system. As a result, some bioinformatics software packaged for the Mac has started to appear.

A list of popular package repositories:

• Biolinux (Fedora)
• BIOrpms (Fedora)
• UMDNJ Informatics Institute (Red Hat Enterprise Linux/Fedora)
• Debian-Med (Debian contains a lot of medical software internally)
• NEBC Bio-Linux (Non-standard Debian)
• RPMfind.net (Various RPM-based distributions, indexed by category)
• Fink scientific packages (Mac OS X)
• Mekentosj (Mac OS X)
• eBiotools and BioX (More than 160 programs and a nice GUI for Mac OS X)

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).

• BioKnoppix
• DNALinux
• Quantian
• Vigyaan
• VLinux
• NEBC Bio-Linux

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

Gentoo Linux provides over 50 bioinformatics applications (see packages.gentoo.org and Gentoo Science Overlay) in the form of ebuilds, 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. Some research institutes, though approving of the distribution, will not install it because they consider that the CPU cycles used for compiling new packages could be better employed for research. It is possible to reduce some of the compilation time by using a central server to generate binary packages, but this drawback should be borne in mind when considering a Gentoo solution.

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 GNU/Linux

There are a few 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

Forum

There is a new forum for BioLinux related topics at BioLinux.com