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
::
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