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

David Adelson david.adelson at tamu.edu
Sun Feb 27 23:43:19 EST 2005


The amount of money they need to spend on computing infrastructure for 
an EST project should be far less than 120K.  Before they spend money 
on hardware they should talk to people who deal with EST data.  Stephen 
Moore is a professor in Edmonton (Animal Science) who does some cattle 
EST work, so your colleagues may want to contact him.   I also have 
some expertise in that area, but there are plenty of others out there 
as well. The real killer in these projects is not building the contigs 
or cluster or doing the BLAST searches, but building the project 
relational db and figuring out how to get the most out of the data.

My $0.02

Dave Adelson
Texas A&M University

On Feb 25, 2005, at 1:26 PM, Gary Van Domselaar wrote:

> Hey Gang,
> I've been called in at the last moment to "consult" on the purchase of 
> a
> cluster for a sequencing project.  Admittedly, I know nothing about 
> life
> science clusters, despite having been subscribed to this list from its
> inception.  I am not making any money on this consulting, just helping 
> out
> a neighbouring academic lab.  So what I know at this point is that they
> 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 
> only
> 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 nicely
> too. The lab currently does not have a bioinforatician, but I thnik 
> they
> have money for one.  I'll probably just end up pointing them to Glen, 
> Joe
> , and Chris, but any advice, suggestions, and pointers to where I can 
> get
> 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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