BioLinux: Difference between revisions

Revision as of 06:41, 23 September 2013

Revision as of 06:42, 23 September 2013

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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 (operating system)|Fedora]] 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 [[RPM Package Manager|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 Linux distributions|SUSE]] use RPMs, so these packages may also work on these distributions.

* BioRPMs<ref>[http://uberh4x0r.org/~yax/biorpm/ BioRPMs]</ref> (RedHat and Fedora)

* RPMfind.net<ref>[http://www.rpmfind.net/linux/RPM/Groups.html RPMfind.net]</ref> (Various RPM-based distributions, indexed by category)

=== Debian ===

[[Debian]] 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 (file format)|deb]] format.

* [[Debian-Med]]<ref>[http://www.debian.org/devel/debian-med Debian Med]</ref> (Debian contains a lot of medical software internally)

* NEBC Bio-Linux<ref>[http://envgen.nox.ac.uk/repository.html NEBC Bio-Linux]</ref> (Non-standard Debian)

=== Slackware ===

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=== Apple/Mac ===

Many Linux packages are compatible with [[Mac OS X]] 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:

* Fink scientific packages<ref>[http://pdb.finkproject.org/pdb/sections.php Fink scientific packages]</ref>

* Homebrew<ref>[http://github.com/mxcl/homebrew Homebrew]</ref>

Similarly, eBioinformatics<ref>[http://www.ebioinformatics.org eBioinformatics]</ref> provides a Mac OS [[GUI]] for over 300 open source bioinformatics programs.<!-- Do all or most of these have origins in Linux? -->

<!-- Removed link to http://www.mekentosj.com/programs/ as connection with Linux seems tenuous -->

== 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<ref>[http://bioknoppix.hpcf.upr.edu/ BioKnoppix]</ref>

* DNALinux<ref>[http://www.dnalinux.com/ DNALinux]</ref>

* Quantian<ref>[http://dirk.eddelbuettel.com/quantian.html Quantian]</ref>

* Vigyaan<ref>[http://www.vigyaancd.org/ Vigyaan]</ref>

* VLinux<ref>[http://bioinformatics.org/vlinux VLinux]</ref>

* NEBC Bio-Linux<ref>[http://nebc.nox.ac.uk/tools/bio-linux NEBC Bio-Linux]</ref>

* BioSlax<ref>[http://www.bioslax.com BioSlax]</ref>

== Standard distributions with good bioinformatics support ==

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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<ref>[http://biolinux.df.ibilce.unesp.br Bio-Linux BR]</ref>

* BioLinux Grupo<ref>[http://biolinux.ourproject.org BioLinux Grupo]</ref>

* NEBC Bio-Linux<ref>[http://envgen.nox.ac.uk/biolinux_doc.html NEBC Bio-Linux]</ref>

* EMBnet.News<ref>[http://www.embnet.org EMBnet.News]</ref> Two issues (2007) dedicated to Bioinformatics Linux distributions

== References ==