[Bio-Linux] Bio-Linux updates

[Dan Swan]

Hi All,

We have taken an updated image this week - for those of you who wish to 
sync your systems against it the image name is:

bio-linux_3.0_650_NVIDIA_19042004

There are a number of updates on this image:

(o)R (the statistical programming language) has been updated to version 
1.9.0.

(o)Bioconductor (microarray analysis package running under R) has been 
updated to version 1.3

(o)We have also fixed the broken protpars link in /usr/software/exec

A major tweak to EMBOSS now allows you to retrieve sequences from remote 
databases, for more information on how to fix this on your own Bio-Linux 
machine see the following links:

http://envgen.nox.ac.uk/envgen/software/archives/000451.html

You will need to download this file:

http://envgen.nox.ac.uk/envgen/software/archives/emboss.default

(o)The latest version of maxdload2 is included in the new image - the 
MIAME compliant database for maxd, the transcriptomics package.

(o)If you wish to check your yum logs recent updates inclde:

cvs 1.11.2-17.i386
ethereal 0.10.3-0.90.1.i386
ethereal-gnome 0.10.3-0.90.1.i386

(o)Newly installed on the image by Yum:

tkinter 2.2.2-26.i386
tix 1:8.1.4-88.i386
itcl 3.2-88.i386

If you are a subscriber to the trade magazine "The Scientist" then 
Bio-Linux has a mention this month in their Open Source Software section:

http://www.the-scientist.com/yr2004/apr/tech_040412.html

For those of you who don't subscribe (and don't wish to sign up on the 
website) I have included the text below (complete with factual 
inaccuracies).  I did try and help the journalist out with clearly 
worded replies to his email enquiries, but he still managed to get his 
wires crossed.  Anyone who has dealt with journalists before will not be 
entirely surprised by this ;)

***
Software Watch | Bioinformatics for the Linux-Curious

If you've been intrigued by Linux but want to avoid the hassle of 
repartitioning your hard drive, Bioknoppix (bioknoppix.hpcf.upr.edu) may 
be just what you need. A bioinformatics-themed version of Knoppix, 
Bioknoppix, unlike most Linux distributions, does not install to the 
hard drive; instead it runs from a CD.

As a result, the existing operating system is untouched, says Bioknoppix 
codeveloper Humberto Ortiz of the University of Puerto Rico. "You just 
pop the CD in and reboot the computer, and up comes Bioknoppix and you 
do your sequence analysis or whatever," says Ortiz. "Then you pop the CD 
out and reboot the computer again," to restore the system. That makes 
Bioknoppix (currently at version 0.2.1 beta) ideal for students, demos, 
and workshops, he says. Users can save their work to a floppy disk, zip 
disk, or a USB pen.

A full-featured Linux variant, Bioknoppix includes such popular titles 
as the KDE graphical user interface and the Open Office productivity 
suite, plus network and programming tools. But it also comes bundled 
with such open-source bioinformatics tools as EMBOSS, ImageJ, ClustalX, 
and bioperl. Other applications will be forthcoming, says Ortiz, 
provided they are both open-source and distributable.

The Bioknoppix download is a hefty 688-MB .iso file ready to be burned 
to disk. At the moment, the team does not provide the software on CD, 
but Ortiz says they may arrange for a vendor to provide that service for 
a nominal fee.

PENGUIN PUSH But bioknoppix is not the only Knoppix-based Linux 
distribution customized for bioinformaticians. Late in march, Pratul K. 
Agarwal of the Oak Ridge National Laboratory released a beta version 
(0.1) of Vigyaan cd. Described on its website (www.vigyaancd.org) as "an 
electronic workbench for computational biology and computational 
chemistry," VigyaanCD (Vigyaan is Hindi for science and knowledge) 
supplements life science tools with chemical ones like XDrawChem and 
Ghemical.

Another Knoppix distribution is expected this fall. The current version 
of Bio-Linux (3.0), available from the UK's national environment 
research council's environmental genomics thematic Programme Data 
Centre, Oxford University, sports a long list of bundled biological 
software. But it also requires a very specific computer configuration: a 
Dell Precision 650, dual 2.4-GHz Xeon CPU workstation with 1 GB RAM, 160 
GB hard disk, and a 17-inch flat-panel display. That's because 3.0 is 
not a true distribution; it is a snapshot, or image, of the installation 
on just such a computer. As a result, according to the Bio-Linux website 
(envgen.nox.ac.uk/biolinux.html), "installing it on hardware that is 
different to ours may cause some initial teething problems." Bio-Linux 
developer Dan Swan says Bio-Linux 4.0, expected in October, will be 
Knoppix-based to eliminate this issue.
**

regards,

Dan


-- 
Dr Dan Swan - Bio-Linux Developer | RHCE
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 658 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk