[Fsf-friends] GNU/Linus distros for life sciences/bioinformatics researchers

[Frederick Noronha (FN)]

Thanks to  "Tarun Kant" <tarunkant@linuxmail.org> and the SunnyLUG from Jodhpur 
for this useful piece of information

For people who are into life science research / bioinformatics, there are a few 
good linux distros available. I will be trying these out in the coming days and 
will keep posting my experiences. These are:

1. DNALinux
DNALinux is a is a SLAX-based Linux distribution with bioinformatics software 
pre-installed. DNA and protein sequence manipulation software is included. Like 
EMBOSS, Primer3, ClustalW, T-Coffe and others.
Website: http://www.dnalinux.com/

2. BioBrew Linux
BioBrew Linux is an open source Linux distribution based on the NPACI Rocks 
(www.rocksclusters.org) cluster software and enhanced for bioinformaticists and 
life scientists. While it looks, feels, and operates like ordinary Red Hat 
Linux, BioBrew Linux includes popular cluster software e.g. MPICH, LAM-MPI, 
PVM, Modules, PVFS, Myrinet GM, Sun Grid Engine, gcc, Ganglia, and Globus, 
*and* popular bioinformatics software e.g. the NCBI toolkit, BLAST, mpiBLAST, 
HMMER, ClustalW, GROMACS, PHYLIP, WISE, FASTA, and EMBOSS. It runs on 
everything from notebook computers to large clusters.
Website: http://bioinformatics.org/biobrew/

3. Bio-Linux
Bio-Linux provides both standard and cutting edge bioinformatics tools on a 
Linux base. It is powerful, configurable and easy to maintain. Bio-Linux 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. As of 
version 4.0, Bio-Linux is based on the  Debian GNU/Linux distribution. 
Bioinformatics-related customisations include the inclusion of a large number 
of bioinformatics programs and programming libraries, the addition of graphical 
menus for much of the bioinformatics software, and links from the desktop to 
key documentation and applications. The system also includes a comprehensive, 
categorised and searchable documentation system for bioinformatics software.

4. Bioknoppix
The University of Puerto Rico High Performance Computing facility (HPCf) and 
the Puerto Rico Biomedical Research Infrastructure Network (BRIN-PR) have 
release Bioknoppix. Bioknoppix is a live CD linux, based on KNOPPIX, and 
specialized to include tools for bioinformatics. Bioknoppix does not need to be 
installed on your computer, making it a perfect tool for workshops and demos. 
Some of the software included in the 0.3 release are EMBOSS 2.8.0, jemboss, 
artemis, clustal, Cn3D, ImageJ, BioPython, Rasmol, Bioperl, Bioconductor
Website: http://bioknoppix.hpcf.upr.edu/

5. Biolinux-BR
BioLinux-BR is a project directed to the scientific community. The intention is 
to create a Linux distribution for people with little familiarity with the 
installation of the operational system and mainly for people that do not know 
how they must proceed to unpack a program, compile and install it correctly. 
For these reasons, this is a Linux system that aims to be easy to use and still 
offering packages that will be part of the BioLinux-BR.
Website:  http://glu.df.ibilce.unesp.br/

6. Vlinux
VLinux Bioinformatics workbench is a Linux distribution for Bioinformatics. It 
is easy to use, no installation required, CD-based distribution based on 
Knoppix 3.3. It includes a variety of sequence and structure analysis 
packages.It is an Open source product released under the GNU GPL License.
Website: http://bioinformatics.org/vlinux/index.html

7. Vigyaancd
VigyaanCD is a live Linux CD containing all the required software to boot the 
computer with ready to use modeling software. VigyaanCD v0.1 is also based on 
KNOPPIX v3.3. It contains programs for bioinformatics, computational biology 
and computational chemistry. It also has genomes from Eschercia coli (K 12) and 
Synechococcus sp. WH 8102 It is suitable both for beginners (12 demos and 
tutorials) and experts. ISO image size (v 0.1) is 647 MB.

And let me tell you this is an effort by an Indian. Kudos to you Pratul K. 
Agarwal for such a nice package. In fact I just downloaded the CD and have 
casually tried it. Looks superb. It has the option for a persistant home 
directory on HDD, which is very essential for Live CDs. Every thing is very 
comprehensively arranged. Once again. Three chers for Pratul.

Cheers -Tarun

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