[Bioclusters] Summary and Thanks for opinions on EST/cDNA assembly, clustering systems

Gary Van Domselaar gary at www.bioinformatics.org
Fri Mar 4 22:53:39 EST 2005

Hey Gang,

I wanted to express my gratitude for all the valuable contributions to my
query about how to best advise on the purchase of a computing system for
EST/cDNA assembly and clustering. The question raised a lot of very
interesting discussion and opinions, including some offline discussion.  
That I can get such high quality advice from the top experts in the field
sp quickly and for free, well it simply blows my mind--huzzah for the
bioclusters list!

Here is how I interpreted the advice.  Hopefully I didnt misinterpret it 
too badly.

1. Don't put the cart before the horse.  Identify the expertise available
to you and the workflow you intend to implement and use that to guide your
hardware purchasing decisions.  This keeps you from looking like a grade
'A' dunce when the critical application you need to run is not compatible
with the system on which you just spent 120 000 dollars. It also allows
you to focus more on the science and less on the IT.

2.  If you have a specific application, build your system around that 
application.  Generic clustering systems may not meet your specific needs 
and can cause lots of grief when you try to hack it to do your specific 

3. Assembly and clustering require lots of memory to run efficiently, so 
64-bit SMP systems with lots of RAM are preferred.

Anyways thanks again to all who contributed.



On Fri, 25 Feb 2005, 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
> _______________________________________________
> Bioclusters maillist  -  Bioclusters at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

More information about the Bioclusters mailing list