[BioC] Thoughts on computer purchase

[Yoder, Sean J.]

Seth is right.  Unless you have other uses for heavy duty video, a
cheapy card will do fine for GeneSpring and BioC as well as pretty much
antyhing you do for an analysis workstation.  I'm running a Dell
Precision 370 with an intel EM64T with 4 GB RAM.  I went with 64 bit for
future Windows 64 uses, but with the intensions of running 64-bit linux
now.  We just ordered another $2500 Dell with similar specs.  I went
with the dual core processor since it was not an expensive upgrade, but
I don't expect it to be of much help...more of a marketing ploy.

You WILL NOT be able to access 4 GB of RAM in Windows for some
reason...I can only get it to recognize 3 GB, and as Seth mentions, most
applications will only access about 1.5GB of RAM at the most...despite
what else you have going on in the background or your Windows memory
settings.

I'd recommend doing a dual boot or having switchable hard drives and
booting into 64-bit Linux with 64-bit BioC for large analyses.  I had a
dual boot setup on this Dell with one HDD and the HDD crashed within a
month and it was a lot of work to get things up and running again...
 
Oh, and a dual monitor setup is great for miroarray or sequence analysis
because you can have your code or your sequences on the extended desktop
and you don't have to swap back and forth when you copy and paste, etc.
I think having two 19" LCDs is much more valuable than upgrading from a
3.0 to 3.2 GHz CPU, for example...plus it makes you look really
important :-)

Good luck,

Sean

Sean Yoder, M.S.
Research Associate
Microarray Core Facility
Moffitt Cancer Center & Research Institute
E-mail:  yodersj at moffitt.usf.edu
Fax:  813-979-7265
Phone:  813-745-1917

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Seth Falcon
Sent: Tuesday, April 25, 2006 10:57 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Thoughts on computer purchase

"Lance Palmer" <lance.palmer at stonybrook.edu> writes:

> I will get to purchase a new computer and have about $3500.  Ijust
wanted
> some advice on a couple options.  Ideally I would want something that
would
> be optimal for things such as Bioconductor and Genespring.
>
>  
>
> In general, I will probably get a system with 4G of RAM and will
probably
> use the 32 bit Windows XP Pro OS.

Are you sure that Windows will be able to use that 4GB of RAM?  If you
read posts to this list and to R-help you will see many threads
discussing how to get a Windows system to access more than 1.5GB or
so.  No such threads for Linux; its memory system is much more useful
for scientific computing.

> If I get the systems lower on the list I could get a 256MB graphics
card,
> instead of 128.  How big of a difference will this make compared to
the
> difference in processor power?  Also I could get two monitors with
some of
> the cheaper processors towards the bottom.  
>
>  
>
> Also I believe the systems towards the top have more maximum memory
> available (if I go to 64 bit system)
>
>  
>
> Any thoughts?

Go with a 64-bit system.  
Consider running a 64-bit flavor of Linux.
Graphics card memory will almost certainly be irrelevant.

+ seth



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