BioLinux: Difference between revisions

Revision as of 19:31, 21 September 2013

Latest revision as of 06:39, 27 May 2025

(31 intermediate revisions by 22 users not shown)

Line 1:

{{Short description|Projects involved in bioinformatics software on Linux}}

{{multiple issues|

{{original research|date=October 2009}}

{{external linksthird-party|date=NovemberSeptember 20122013}}

}}

{{third party}}

'''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:

Line 10 ⟶ 13:

* 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] {{webarchive |url=https://web.archive.org/web/20051215114230/http://gchelpdesk.ualberta.ca/news/03mar05/cbhd_news_03mar05.php#GearingUp |date=December 15, 2005 }}</ref> that details some of the Linux-based projects.

== Complete systems ==

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

* BioBrew<ref>[http://bioinformatics.org/biobrew/ BioBrew]</ref>

* BioLand<ref>[http://bioland.cbi.pku.edu.cn/ BioLand]</ref>

* 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>

* OSDDlinux<ref>[http://osddlinux.osdd.net OSDDlinux]</ref>

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

== Package repositories ==

=== Red HatApple/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:(source?)

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.

=== BioArchLinux ===

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

[https://github.com/BioArchLinux/Packages BioArchLinux repository] contain more than 3,770 packages for Arch Linux and Arch Linux based distribution. <ref name="Zhang 2025">{{Cite journal|last1=Zhang|first1=Guoyi|last2=Ristola|first2=Pekka|last3=Su|first3=Han|last4=Kumar|first4=Bipin|last5=Zhang|first5=Boyu|last6=Hu|first6=Yujin|last7=Elliot|first7=Michael G|last8=Drobot|first8=Viktor|last9=Zhu|first9=Jie|last10=Staal|first10=Jens|last11=Larralde|first11=Martin|last12=Wang|first12=Shun|last13=Yi|first13=Yun|last14=Yu|first14=Haoran|date=2025|title=BioArchLinux: community-driven fresh reproducible software repository for life sciences|journal=Bioinformatics|pages=btaf106|doi=10.1093/bioinformatics/btaf106|issn=1367-4811|doi-access=free|pmc=11925497}}</ref>

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

=== Debian ===

Line 37 ⟶ 28:

[[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.

=== Apple/MacRed Hat ===

* [[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)

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.

=== Slackware ===

Line 45 ⟶ 37:

* [[BioSLAX]]

=== 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 ==

Line 74 ⟶ 48:

; Gentoo Linux

[[Gentoo Linux]] provides over 50156 bioinformatics applications (see [http://packagesgpo.gentoozugaina.org/packages/?category=sci-biology packages.gentoo.org]Gentoo andsci-biology [http://overlays.gentoo.org/proj/scienceherd Gentooin the Sciencemain Overlaytree]) in the form of [[ebuild]]s, which build the applications from source code. Additional 315 packages are in [https://gitweb.gentoo.org/proj/sci.git 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]] is not a Linux distribution, but as it is a version of [[BSD|Unix]] that it is very similar. Its [[ports collection|ports]] are likeanalogous Gentoo's ebuilds, and the same caveats apply. However, therethe areproject alsocontinuously builds pre-compliedcompiled binary packages available.for ThereTier-1 areplatforms oversuch 60as biological[[x86]] sciencesand applications,[[ARM_architecture_family|ARM]]. Users can also choose to build and they'reinstall listedany onport thefrom Freshsource Ports<ref>[http://wwwin order to enable non-portable optimizations or other build options.freshports.org/biology/ Fresh Ports]</ref>The build-from-source option also allows the ports system to automate installation of software with a license that does not permit siteredistribution.

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<ref>[http://www.freshports.org/biology/ Fresh Ports]</ref> site.

; pkgsrc

The [[pkgsrc]] package manager, originally forked from [[FreeBSD ports]], is maintained by the [[NetBSD]] project, but aims to support all [[POSIX]]-compatible operating systems. It is well-tested on [[NetBSD]], many [[Linux]] distributions, [[macOS]], and [[SunOS]] 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<ref>[{{Cite web |url=http://envgen.nox.ac.uk/biolinux.html |title=NEBC Bio-Linux] |access-date=2005-12-19 |archive-date=2006-04-22 |archive-url=https://web.archive.org/web/20060422152024/http://envgen.nox.ac.uk/biolinux.html |url-status=dead }}</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 ==

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.

== See also ==

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

* [[List of open-source bioinformatics software]]

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

* [[List of biomedical cybernetics software]]

* 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|colwidth=30em}}

{{Free healthcare software}}

{{DEFAULTSORT:Biolinux}}

[[Category:Bioinformatics software]]

[[Category:Linux]]

[[Category:Computational science]]