Another Linux success. -- Jason Hayes - Principal Hayes Holdings Consulting [EMAIL PROTECTED] / www.hayz.ws Suite #1936 - 246 Stewart Green SW Calgary, AB, Canada T3H 3C8 Ph: 403.260.5202
http://www.the-scientist.com/yr2004/apr/tech_040412.html Volume 18 | Issue 7 | 37 | Apr. 12, 2004 Front Page Bioinformatics for the Linux-Curious; Mining for Microbial Community Insights 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. --Jeffrey M. Perkel _______________________________________________ clug-talk mailing list [EMAIL PROTECTED] http://clug.ca/mailman/listinfo/clug-talk_clug.ca
