BioLinux: Difference between revisions

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

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{{original research|date=October 2009}}

{{external links|date=November 2012}}

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* 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.

== 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. (source?)

=== BioArchLinux ===

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.

[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>

=== 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.

=== Apple/MacRed 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.

=== Slackware ===

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* [[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. (source?)

== Live DVDs/CDs ==

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; 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 ==

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

* [[List of biomedical cybernetics software]]

== References ==

{{Reflist|colwidth=30em}}

==External links==

{{Free healthcare software}}

[[Category:Bioinformatics software]]

[[Category:Linux]]

[[Category:Computational science]]