[BioC] Computer for the analysis of high-throughput genomic data

[Capurro, Alberto (Dr.)]

Thank you very much. I will do microarray analysis at first but in the future we are also interested in sequencing. The computer is for the lab, I will be in charge of the processing, I have experience in computational neuroscience but not in genomics, so I am learning now. I think that the Uni  usually buys windows machines. Regarding the operating system, is there an important reason to use linux instead of windows 7 to run bioconductor and R?. I can use linux if it is better. I can get 10 T and backup in and external disk and in space provided by the Uni network. 

Thank you very much.

Best,

Alberto

Alberto Capurro
Marie Curie Research Fellow
Department of Cell Physiology and Pharmacology
College of Medicine, Biological Sciences and Psychology
Maurice Shock Medical Sciences Building Room 319
University of Leicester
Leicester LE1 9HN
United Kingdom

Tel +44 (0)116 252 2673
E-mail: ac331 at le.ac.uk
https://sites.google.com/site/albertocapurro/
________________________________________
From: Steve Lianoglou [mailinglist.honeypot at gmail.com]
Sent: Thursday, December 27, 2012 8:55 PM
To: Capurro, Alberto (Dr.)
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Computer for the analysis of high-throughput genomic data

Hi,

On Thu, Dec 27, 2012 at 11:14 AM, Capurro, Alberto  (Dr.)
<ac331 at leicester.ac.uk> wrote:
> Hello,
>
> I would need to purchase a desktop computer for the analysis of high-throughput genomic data using R/Bioconductor. I want to ask you the specifications that I should look for (as for example ram memory, processor type, number of cores). Can you mention specific examples of state of the art machines fitted for this purpose?

This is a hard question to answer.

Is the machine for yourself, or a lab, more users?

What types of analysis will you be doing? Will you be working with raw
NGS data -- if so, just sequence alignment, assembly, etc? Do you have
a compute cluster to push those types of jobs over to?

Anyway -- absent any of that information, for us mere mortals who shop
at "pro-sumer" levels, I wouldn't complain too much if I had, say, a
12 core, 32-64gb ram osx or linux machine sitting underneath my desk.

If you're working w/ NGS data, no matter how much HD space you get,
you will always run out, so you will constantly have to be adding
upgrades there, but start with several terabytes ... also ... you'll
have to think about how you plan to backup your data, but I'll leave
that as another topic.

But, as I said, the more (of everything) the merrier.

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact