[Bioclusters] Need some advice on a cluster for EST/cDNA assembly, clustering

Brodie, Kent brodie at mcw.edu
Fri Feb 25 15:03:59 EST 2005

There's so many choices in this area it's difficult to recommend one
single solution.   In general terms however, there will be easier setup
and deployment with Linux than Sun; (for example, with most Linux
distributions, gcc and compiling tools and such are all built in).   Sun
has great hardware, but the overall maintenance costs will be a huge
factor.    With cheaper x86 boxes for example, you could have a whole
lot of compute nodes, and not worry too much about support costs
("throwaway" boxes?).

A lot of it also depends on the in-house operating system expertise they

That's my $0.02.     

> -----Original Message-----
> From: bioclusters-bounces+brodie=mcw.edu at bioinformatics.org
> [mailto:bioclusters-bounces+brodie=mcw.edu at bioinformatics.org] On
> Of Gary Van Domselaar
> Sent: Friday, February 25, 2005 1:26 PM
> To: bioclusters at bioinformatics.org
> Subject: [Bioclusters] Need some advice on a cluster for EST/cDNA
> assembly,clustering
> Hey Gang,
> I've been called in at the last moment to "consult" on the purchase of
> cluster for a sequencing project.  Admittedly, I know nothing about
> science clusters, despite having been subscribed to this list from its
> inception.  I am not making any money on this consulting, just helping
> a neighbouring academic lab.  So what I know at this point is that
> have about $Cdn 200K to spend.  They hae already talked to Sun, and
Sun is
> offering them a "sweetheart" deal for (something) at about $120k.  My
> exposure is to a G4/G5 cluseter from BioTeam.  I am impressed with it
> andit works really well for my purposes, and Im guessing it would work
> well for theirs too.  I'm guessing a linux cluster would perfrom
> too. The lab currently does not have a bioinforatician, but I thnik
> have money for one.  I'll probably just end up pointing them to Glen,
> , and Chris, but any advice, suggestions, and pointers to where I can
> a little more familiarity, well shucks, that would really be swell.
> Decidedly,
> g.
> --
> Gary Van Domselaar, PhD.
> Postdoctoral Fellow, Computing Science
> and Biological Sciences
> University of Alberta
> Edmonton, AB, Canada
> Phone: 780-492-5969
> Assistant Director, Bioinformatics.Org
> gary at bioinformatics.org
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