Content deleted Content added
→Slackware: Grammar |
Sarahj2107 (talk | contribs) Replaced inline external links with ref, removed tag |
||
Line 1:
{{
'''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]]/[[CD]]s 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<ref>[http://gchelpdesk.ualberta.ca/news/03mar05/cbhd_news_03mar05.php#GearingUp overview in the Canadian Bioinformatics Helpdesk Newsletter]</ref> that details some of the Linux-based projects.
== Complete systems ==▼
▲==Complete systems==
Various complete distributions that integrate bioinformatics software are available, in various stages of development.
*[http://bioinformatics.org/biobrew/ BioBrew]▼
*[http://bioland.cbi.pku.edu.cn/ BioLand]▼
*[http://biolinux.df.ibilce.unesp.br/ BioLinuxBR]▼
*[http://www.bioslax.org/ BioSLAX]▼
*[http://www.debian.org/devel/debian-med/ Debian Med]▼
*[http://envgen.nox.ac.uk/biolinux.html NEBC Bio-Linux]▼
▲* BioBrew<ref>[http://bioinformatics.org/biobrew/ BioBrew]</ref>
==Package repositories==▼
▲* BioLand<ref>[http://bioland.cbi.pku.edu.cn/ BioLand]</ref>
===Red Hat===▼
▲* BioLinuxBR<ref>[http://biolinux.df.ibilce.unesp.br/ BioLinuxBR]</ref>
▲* BioSLAX<ref>[http://www.bioslax.org/ BioSLAX]</ref>
▲* Debian Med<ref>[http://www.debian.org/devel/debian-med/ Debian Med]</ref>
▲* NEBC Bio-Linux<ref>[http://envgen.nox.ac.uk/biolinux.html NEBC Bio-Linux]</ref>
▲== Package repositories ==
▲=== 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 (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.
*[http://uberh4x0r.org/~yax/biorpm/ BioRPMs] (RedHat and Fedora)▼
*[http://www.rpmfind.net/linux/RPM/Groups.html RPMfind.net] (Various RPM-based distributions, indexed by category)▼
▲* BioRPMs<ref>[http://uberh4x0r.org/~yax/biorpm/ BioRPMs]</ref> (RedHat and Fedora)
===Debian===▼
▲* 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.
*[http://www.debian.org/devel/debian-med Debian Med] (Debian contains a lot of medical software internally)▼
*[http://envgen.nox.ac.uk/repository.html NEBC Bio-Linux] (Non-standard Debian)▼
▲* Debian Med<ref>[http://www.debian.org/devel/debian-med Debian Med]</ref> (Debian contains a lot of medical software internally)
===Slackware===▼
▲* NEBC Bio-Linux<ref>[http://envgen.nox.ac.uk/repository.html NEBC Bio-Linux]</ref> (Non-standard Debian)
▲=== Slackware ===
[[Slackware]] is one of the less used [[Linux distribution|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.
*[[BioSLAX]]▼
▲* [[BioSLAX]]
===Apple/Mac===▼
▲=== 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:
*[http://pdb.finkproject.org/pdb/sections.php Fink scientific packages]▼
*[http://github.com/mxcl/homebrew Homebrew]▼
▲* Fink scientific packages<ref>[http://pdb.finkproject.org/pdb/sections.php Fink scientific packages]</ref>
Similarly, [http://www.ebioinformatics.org eBioinformatics] provides a Mac OS [[GUI]] for over 300 open source bioinformatics programs.<!-- Do all or most of these have origins in Linux? -->▼
▲* 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).
*[http://bioknoppix.hpcf.upr.edu/ BioKnoppix]▼
*[http://www.dnalinux.com/ DNALinux]▼
*[http://dirk.eddelbuettel.com/quantian.html Quantian]▼
*[http://www.vigyaancd.org/ Vigyaan]▼
*[http://bioinformatics.org/vlinux VLinux]▼
*[http://nebc.nox.ac.uk/tools/bio-linux NEBC Bio-Linux]▼
*[http://www.bioslax.com BioSlax]▼
▲* BioKnoppix<ref>[http://bioknoppix.hpcf.upr.edu/ BioKnoppix]</ref>
==Standard distributions with good bioinformatics support==▼
▲* 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 ==
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]] provides over 50 bioinformatics applications (see [http://packages.gentoo.org/packages/?category=sci-biology packages.gentoo.org] and [http://overlays.gentoo.org/proj/science Gentoo Science Overlay]) in the form of [[ebuild]]s, which build the applications from source code.
Line 62 ⟶ 76:
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 [[BSD|Unix]] it is very similar. Its [[ports collection|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<ref>[http://www.freshports.org/biology/ Fresh Ports]</ref> site.
; Debian
There are more than a hundred bioinformatics packages provided as part of the standard Debian installation. NEBC Bio-Linux<ref>[http://envgen.nox.ac.uk/biolinux.html NEBC Bio-Linux]</ref> 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 ==▼
▲==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<ref>[http://biolinux.
* 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 ==
{{Reflist}}
{{DEFAULTSORT:Biolinux}}
[[Category:Bioinformatics]]
[[Category:Linux]]
| |||