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

Matthew Hudson mhudson at uiuc.edu
Mon Feb 28 10:42:19 EST 2005

Another key consideration is: How much sysadmin experience / effort does 
this life science group have? Maintaining and updating a Linux cluster 
built from scratch can be a challenge for a group of biology PhDs with no 
full-time sysadmin, not to mention the cost of power consumtion, cooling 
etc.. Sun is a little better than building your own Linux system, Apple 
really try to make this easier and might be a better solution, but their 
cluster software is expensive. If it's just an EST project you might 
recommend they get one or two good size SMP machines (maybe the new quad 
Opterons from Sun, with at least 8GB RAM) and forget about the cluster.

At 10:43 PM 2/27/2005, David Adelson wrote:
>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.
>>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
>>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>Bioclusters maillist  -  Bioclusters at bioinformatics.org

Matthew Hudson
Assistant Professor of Genomics
Department of Crop Sciences
University of Illinois
334 National Soybean Research Center,
1101 W. Peabody
Urbana, IL 61801, United States.
Phone 217 244 8096, email mhudson at uiuc.edu

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