Linux vs Unix for doing bioinformatics

Steffen Schmidt schmidt at embl-heidelberg.de
Wed Mar 1 11:31:13 EST 2000


Stephane Bortzmeyer wrote:
> 
> In article <Pine.SOL.3.96.1000225113218.4072V-100000 at cress>,
>  Keith Bradnam <keith at thale.nott.ac.uk> writes:
> 
> > 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?
> 
> The Subject: is incorrect. Linux is an Unix, like a dog is a mammal or
> an applepie is a pie.
> 
> And you have to distinguish hardware and software. I ran blast on an
> Alpha/Linux. Linux is not PC-specific and the Alpha do not always run
> Tru64 (formerly Digital Unix).
> 
> > 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.
> 
> Did you consider FreeBSD-on-PC also? (No, I didn't try myself but I'm
> interested if someone did.)

We are running BLAST searches on Linux based PentiumIII-Servers - we
have severe problems (i.e. the server crashes) when we use e.g. blastpgp
and a database which is accessed via NFS. This is a known bug to Linux
as far as I know (If someone knows better please answer). So the best
way to use BLAST is by using locally stored databases and everything is
fine!





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