Linux vs Unix for doing bioinformatics

Dr. Greg Quinn greg at franklin.burnham-inst.org
Wed Mar 1 12:50:46 EST 2000

A lot of folks are using Linux for intensive bioinformtics uses, and I've 
recently started to do this on a quad pentium box; it seems to work well, 
but as the other responder suggested, there are problems. My gut feeling 
is that the implementations of Linux you'll likely to be using are not 
really to the level of commercial software such as Intel Solaris. I got a 
communication a while back from some folks at NCBI in which they 
indicated that they were or had set up clusters of pentiums for running 
blast jobs, but using X86 Solaris. A big practical advantage for Linux is 
that bioinformatics executables for Linux are everywhere, but rarely 
found for X86 Sol, or FreeBSD (another UNIX flavor which ISP's use on 
pentiums; generally, for a bunch of reasons including stability, security 
and ability to handle high load, ISP's don't touch solaris). Another big 
problem is that Linux doesn't have a reliable version of the 'dump' 
program, so you're usually left backing up with tar (taper, etc), which 
isn't a wonderful alternative. To be honest, if I was starting from 
scratch again (and I may do that), I wouldn't use Linux, but Solaris X86 
or FreeBSD..... probably Solaris, which is free to academics now.
My 0.02c

Keith Bradnam (keith at thale.nott.ac.uk) wrote:
: Hello,
: Does anybody have any experience of performing intensive bioinformatics
: tasks (e.g. running blast searches, serving databases to the outside
: world) on PCs running linux as oppposed to Suns or DECs?
: We are currently looking to upgrade our Sun servers and are curious
: whether switching to Linux on high-end PCs is a better (and maybe cheaper)
: option for doing bioinformatics.
: Thanks in advance,
: Keith
: ~  Keith Bradnam - Developer, Arabidopsis Genome Resource (AGR)
: ~  Nottingham Arabidopsis Stock Centre - http://nasc.nott.ac.uk/
: ~  University Park, University of Nottingham, NG7 2RD, UK
: ~  Tel: (0115) 951 3091 

Computational Biology Group
The Burnham Institute
(formerly La Jolla Cancer Research Inst.)
10901 North Torrey Pines road
La Jolla
Phone:(619) 646 3103
Email: greg at franklin.ljcrf.edu

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