Wikiomics:Specialized Linux distributions

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Also see Wikiomics:Linux packages for software repositories specializing in bioinformatics packages.


There is a high attrition rate for specialized towards bioinformatics Linux distributions, so large number of them is at this stage of historic value only. Some of them may rise from the ashes i.e morphing into virtual desktops/servers like DNALinux. As for Feb 2010 you will be better of sticking to some stable, well maintained general purpose distro (Debian, Ubuntu, Fedora, or Rocks Linux for a cluster) and either install individual prepackaged programs from repositories (be aware that these almost always are at least one version behind, i.e. you get EMBOSS 6.1 from 15-Jul-2009 and not EMBOSS 6.2 available since 15-Jan-2010) or install it from original sites.


Contents

Viable distros

NEBC Bio-Linux

NEBC Bio-Linux provides both standard and cutting edge bioinformatics tools on a Ubuntu base. It is powerful, configurable and easy to maintain. It has been customised for ease of use and provides an ideal system for scientists handling and analysing biological data. Bio-Linux also comes with many development tools, providing a solid base for bioinformatics software development. It can also be easily deployed as a computer cluster. A Live NEBC Bio-Linux DVD is also available.

Provides tools for next generation sequencing.

Latest release: June 4, 2010

Rocks Linux

Rocks Linux it is a powerful cluster distro with a bioinforatics "roll" (an optional set of utilities to install). Based on CentOS.

Latest release: 5.3.0 16-12-2009

DNALinux

DNALinux is a Slax based Live CD with bioinformatic programs. Since it uses RAM instead or harddisk, the user has the option to load a lightweight GUI (Xfce) or the full featured KDE. It is developed at the Universidad Nacional de Quilmes.

Update Feb 2010: distributed as virtual desktop running on top of VMware

JCVI Cloud Bio-Linux

Virtual distro capable of using Amazon EC2 and Eucalyptus, based on 64-bit Ubuntu. Large library of bioinformatics software

Biopuppy Linux

Small (270MB) live CD distribution: http://www.biopuppy.org/ Latest release: 2.0 (Nov 2009)

PhyLIS

site: http://www.eve.ucdavis.edu/rcthomson/phylis/

Phylogeny-oriented distro based on Ubuntu 8.04 LTS Desktop. Last update: June 2009

Open Discovery

site: http://www.opendiscovery.org.in "capable of booting from USB drives and the changes persist over reboot, i.e you can modify and store data within the USB-drive" (quote from http://www.bioinformatics.org/forums/forum.php?forum_id=7020)


BioconductorBuntu

BioconductorBuntu: implements a web-based DNA microarray analysis server. May 2009?

History (?)

BioKnoppix

BioKnoppix is a customized distribution of Knoppix Linux Live CD. With this distribution you just boot from the CD and you have a fully functional Linux OS distribution with open source applications targeted for the molecular biologist. Beside using some RAM, Bioknoppix doesn't touch the host computer, being ideal for demonstrations, molecular biology students, workshops, etc.

BioBrew

From the BioBrew web page: "BioBrew is a collection of open-source applications for life scientists and an in-house project at Bioinformatics.Org. The BioBrew Roll for Rocks can be used to create Rocks/BioBrew Linux, a distribution customized for both cluster and bioinformatics computing: it automates cluster installation, includes all the HPC software a cluster enthusiast needs, and contains popular bioinformatics applications."

Latest release: 2006


APBioKnoppix

APBioKnoppix (moved to Linux users in the National University of Singapore) is a LiveCD containing all commonly used bioinformatics software packages such as EMBOSS pre-installed on the Knoppix Debian Linux platform, compressed into a bootable CD for intel PCs.

VLinux

Knoppix-based portable Live CD for Bioinformatics. http://bioinformatics.org/vlinux

Vigyaancd

http://www.vigyaancd.org/ Another Knoppix-based portable Live CD for bioinformatics


Quantian

Last relase: 2006

Quantian is a remastering of Knoppix. Quantian also incorporates clusterKnoppix and adds support for openMosix, including remote booting of light clients in an openMosix terminal server context.

Some introductory material on Quantian is available in an article in the Political Methodologist. The bioinformatics capabilities of Quantian were addressed in the June 30, 2005 issue of the Canadian Bioinformatics Helpdesk Newsletter.

Debian-Med

Debian-Med is a package of programs that can be installed easily on a Debian GNU Linux system. While not a distribution per se, Debian-Med is a good method of converting a standard Linux distribution into a system ready for many bioinformatics tasks.


Articles reviewing Linux distributions customised for bioinformatics (old)

Gearing Up for Bioinformatics, Canadian Bioinformatics Helpdesk Newsletter, March 3, 2005

Gearing up for Bioinformatics, 2004 Linux User and Developer, 46, 50-56

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